Setting up Tables for Coplanarity
Set the infeed and outfeed tables to the same height relative to one another (and a hair higher than the knives/cutterhead). Check the table's Gib bolts (if a traditional dovetailed ways jointer table) so that the tables can be smoothly raised and lowered without too much resistance, but tight enough that there is no excess free-play within the dovetailed ways the tables travel upon. The tables should be level all the way across when your straightedge is placed on the front, then rear of the tables (with the straightedge straddling both the infeed and outfeed). Now check that the diagonals are also level across their width by using the straightedge to check the diagonals while straddling both tables.
You will likely want a feeler gauge with 0.002" to 0.004" blades -- barring a feeler gauge, a flashlight behind the straightedge can be used to look for light showing under the straightedge. Ideally you don't want any significant areas where you can fit the feeler gauge between the straightedge and the jointer tables. Note that the jointer tables may have high and low spots that complicate measurement some, but what really matters is the overall levelness/coplanarity so minor high and low spots (a couple mils) generally causes no issues with woodworking and is within the manufacturing tolerances for a jointer.
If you find that the tables are not coplanar over their width along their lengths front and back and the two diagonals then you will need to make adjustments to bring the tables into a uniform levelness over their combined length. Some jointers, such as parallelogram models, have built in adjustments to correct for this error (refer to your manual). Most traditional jointers, though, use dovetailed ways and provide for no such adjustment. To adjust such jointers you will need to invest in some BRASS shim-stock (stainless steel would be Ok as well, but not paper, plastic or aluminum shims) with 0.001", 0.002", 0.003" and 0.005" thicknesses (Hobby Shops and some Ace stores often carry this shim-stock) to shim the corners of the table (or tables) along the dovetailed ways. If the error is minor, it is most practical to declare one of the tables (either infeed or outfeed) as 'fixed' and then shim the opposite table until it is coplanar with that table. Generally, it is best to shim the outfeed table since it is seldom adjusted and places the least wear on the shims, but either table can be shimmed. If the error is great then you will likely have to shim both tables until the overall error over their lengths and diagonals becomes acceptable.
Don't forget to tighten the tables' Gib bolts after each shimming and before each measurement with your straightedge. The Gib bolts should be tight enough to eliminate any free-play when raising/lowering each table, but not so tight as to significantly impair raising and lowering each table -- a little resistance is fine but you should not have to struggle to raise or lower the tables. You will have to loosen the gib bolts and slightly lift each table to insert the shim-stock (I recommend you leave at least 1/4" of shim extending out when you place your shims so that you can easily remove or replace them in the future if need be. When done, I bend these 1/4" tabs downward so they don't catch on anything and the shims don't get drawn further into the ways. It is really critical to re-tighten the Gib bolts after placing your shims before you recheck levelness/coplanarity because the free-play in the tables, coupled with the effects of gravity, will cause the tables' ends to dip downward and their opposite end, nearest the knives will, in turn, tip upward, fouling up your measurements if you fail to tighten things down before rechecking.
Once the tables are coplanar with one another, you will next need to setup the cutterhead such that it is coplanar with the tables.
NOTE: It is possible to avoid this if you always reference knife height against the outfeed table, but it is still best to set the cutterhead coplanar to the tables. If you have Quickset (spring-loaded) knives then coplanarity of the cutterhead to the tables is critical, and non-optional, since the knives will be set at a constant height relative to the cutterhead, not the outfeed table.
You can either use a good straightedge (if your tables are fairly flat, even a stiff and straight 12-18" steel or aluminum ruler (such as from a combination square) or you can use the more accurate dial-indicator with either a magnetic base jig or a commercial or DIY mount that squarely references the dial to the outfeed table allowing you to measure the height of the CUTTERHEAD (not knives) relative to the outfeed table.
If you go the straightedge route, lower the outfeed table until the straightedge just barely grazes/misses the highest point of the cutterhead. This high-point becomes your reference point (since it cannot be made lower). We will then have to raise the lower end of the cutterhead until it, too, is even with the outfeed table, and this we can do with some more shims.
If this is a traditional jointer, there will be a bolt that holds the bearing's pillow block that extends to the bottom of the jointer bed (there is usually a cutout in the center of the Jointer's central frame located directly below the cutterhead. You will need an appropriate sized wrench to loosen this bolt. You may also need to loosen the bolt on the high side to get enough play to insert shims on the low end.
Once the pillow blocks have been loosened a bit, you will then place two brass shims (of equal thickness) at about the 4:30-o'clock and 7:30-o'clock positions under the pillow block. You will have to guesstimate the shim thickness, but start with a shim that is roughly equal to the gap between the cutterhead and the outfeed table (at the low end). Next, re-tighten the pillow block bolts to re-secure the cutterhead. I SHOULD ALSO MENTION THAT YOU WILL LIKELY NEED TO EITHER DE-TENSION OR REMOVE THE BELT SO THAT YOU CAN INSERT YOUR SHIMS. Re-measure the cutterhead to see if it is now parallel. If it is too high then you can reduce the thickness of your shims, it is too low then increase the shim thickness, then re-tighten and recheck until you are within 0.001" over the length of the cutterhead.
Once the cutterhead is coplanar with the outfeed table it should also, by logical extension, now be coplanar with the infeed table since the two tables should already be coplanar with each other.
Now you can raise your outfeed table to allow for an appropriate amount of knife protrusion (typically 1/8" to 1/4", with 3/16" a good starting point) above the cutterhead to allow for good chip clearance.
Setting Quickset Knives
If you have Quickset (spring loaded) knives then your jointer should have included a special jig that will press the knives inward until they are an appropriate height above the cutterhead (a height that should be even across the cutterhead's length). You will press this jig into the knives while you tighten two of the gib bolts (one towards each end) to hold the knife in position. Then remove the setting jig and securely tighten the remaining gib bolts. Repeat for each of the knives. When all of the knives have been set, you will want to carefully set the height of the outfeed table until it is exactly even with the highest point in the knife's travel (aka TDC or Top Dead Center). The knives should be within 0.001" over the width of the cutterhead and equally within 0.001" over their width relative to the outfeed table. If need be, you can lower the outfeed table by up to 0.001" below the knives' TDC, but no more.
Setting Traditional Loose Knives
If you have more traditional knives (not spring loaded), then you will want to use a magnetic jig (either commercial or DIY) that holds the knives at a consistent height at TDC (top dead center = highest point of the knife's travel) relative to the outfeed table. Since the knives are being set relative to the outfeed table the height of the outfeed table above the cutterhead will determine the amount to which the knives protrude above the cutterhead (1/8" to 1/4" -- aim for 3/16"). With the magnetic jig holding each knife at the proper height at TDC, carefully tighten two gib bolts (one towards each end) to secure the knife, taking care not to alter the height at which the magnetic jig is holding your knives AND without accidentally rotating the cutterhead off of TDC. With the knife securely held in alignment, tighten all the remaining gib bolts (the first two bolts you tightened will prevent you from knocking the knife out of alignment). With such a jig, all 2-4 knives will be set to the same protrusion above the cutterhead and should be perfectly parallel to, and even with, the outfeed table.
Now that the knives are set parallel and coplanar to one another and infeed and outfeed tables. Go ahead and double-check that the outfeed table is perfectly parallel to each knife (or at least the highest knife) at TDC. You can either leave the outfeed table perfectly level with your knives or it can be set up to 0.001" below the knives depending upon what your past experience suggests works best for you.
Once the tables, cutterhead, and knives have all been addressed, there is still one more setup task remaining: the fence. Using an accurate square (or triangle) you will want to adjust the fence so that it is perfectly perpendicular (90deg) relative to both the infeed and outfeed tables (which should be easy if the two tables are coplanar). Keep in mind, however, that because tables are not always ground perfectly flat, you will want to recheck the fence's alignment whenever you adjust the fence (as in, move it in or out). You can also take the time to setup the 45deg, 90deg and 135deg stops if you wish -- just keep in mind that they, too, can vary a little as you move the fence in or out to adjust its position along the tables' width (such as when wear-leveling the knives during edge jointing) -- so always recheck the fence's alignment after each repositioning.
On Setup Tools
The initial setup of a new jointer can be a fair bit of work -- especially if the tables do not arrive already coplanar -- but fortunately it is a one time job. The tools required, such as the precision straightedge(s), feeler gauges, and dial indicators (and their mounts) do add a bit to the initial cost, but they are an investment that will pay off many times over as you use them over and over again to setup your other power tools as well as to periodically recalibrate and verify the calibration of your power tools over the years.
A Note on Straightedges
Depending on your budget you can either purchase a good quality precision machinist straightedge (though they are not cheap) or you can look for suitably adequate (by woodworking standards) straightedges in other tools or materials. I own a precision 2ft aluminum straightedge, but my 4' straightedge is a box level with a machine ground face that the manufacturer guarantees to be within +/- 0.002" across its length -- plenty good enough by woodworking standards.
Once your jointer is properly setup, you should not have to invest any more setup time (other than blade changes) unless something causes a significant drift in your original setup (e.g. a hard impact, someone trying to lift the jointer by its tables, etc.). With the proper setup tools, you will be able to quickly determine if such accidents have knocked things out of alignment and, if so, readjust as necessary. This goes not just for jointers, but for any precision tool in your arsenal, so it is well worth the initial investment to acquire these setup tools.
Common Complaint: My Jointer is Cutting Tapers!
Whenever your jointer starts cutting tapers you need to check the height of your outfeed table relative to the height of your highest knife (ideally all knives are the same height). If the table is a little too high (no more than a few thousandths of an inch) you will cut tapers that are thinnest at the start of the cut and thickest towards the end of the cut (in fact, you will likely find it difficult to joint the final inches of the board on a given pass if it is off by much). If the outfeed table is too low, you will get the opposite effect, a thicker board at the start of the cut and thinnest towards the end.
Practically speaking, the outfeed table cannot be more than a couple thousandths too high or your board will run into the leading edge of the outfeed table and come to a stop (unless the edge has been chamfered). The opposite problem, an outfeed table too low, does not have the same limitation and can be further off without inhibiting otherwise normal operation.
Now if your board is tapering across its width, rather than its length, then either your tables are not coplanar to one another OR your knives are not coplanar with the tables (that is to say, the knives are high at the front/back of the jointer and lower at the opposite end). You can check whether your tables are coplanar by using a quality straightedge (preferably at least 4ft, 6ft is even better) and setting the infeed and outfeed tables level with each other.
When everything has been setup properly, you should find your jointer to be a reliable means by which to face joint, edge joint, and square your lumber and the perfect companion to the thickness planer. The jointer will give you two flat and square faces (face plus edge) to then feed the thickness planer which, in turn, gives you an opposite, parallel, face that is also flattened and uniformly thicknessed.