The good news is that the type of slot you'll be creating is pretty much the most difficult type of biscuit joinery, so once you master it you will have pretty much mastered biscuit joinery. Fortunately, if you take a little bit of time to lay things out and think out your references, it really isn't terriibly difficult, just a little nerve wracking for the first timer is all.
For this type of joinery you typically reference against the
bottom of the biscuit joiner (rather than the fence like you do with edge joinery).
THE MOST IMPORTANT POINT TO REMEMBER: THE OFFSET FROM THE BASE IS EXACTLY 3/8" ON CENTER! If your carcase is 3/4" thick, then this conveniently centers the biscuit for you. If it is at least 5/8" thick to around 1" thick, you can safely install the biscuits off center if you wish to simplify the layout. If your carcase is less than 5/8" or much more than 1" thick, then you will need to go to the extra effort to lay things out appropriately and calculate your positive or negative offsets and starting pionts.
To begin, match your faceframe to the carcase and clamp it, centered and aligned according to your specs or design. Take a pencil and trace the outline of the carcase on the backside of the faceframe (when you are done you can erase any excess pencil lead from the perimiter of the
carcase, but make sure you leave a good, clean, solid line on the backside of the faceframe). You'll want this pencil line to be as narrow and sharp as possible (sharp pencil point, or a 0.5 to 0.7mm pencil). This line will show you the outline of your carcase on the faceframe providing you with a point of reference for calculating your offset (if needed) OR referencing the base of your biscuit joiner IF the 3/8" offset is compatible with your carcase as-is.
Just to confuse things a bit: If you are certain the offset is precisely 1/16" (and not just thereabouts) then you could use the fence like you are familiar with, centered for the carcase, then carefully adjusted 1/16" for the faceframes -- but only if the overhang is a perfect 1/16" all the way around. I'm not sitting in front of my PC biscuit joiner right now, but my guess is that 1-1/2 to 2 turns probably equals 1/16" (the threads are likely about 24-32 tpi) -- but test your offset before you go this route or you may encounter alignment issues.
Once you have any necessary positive or negative offsets calculated, clamp or tape (with double-sided tape -- you could also use 23ga pins with minimal penetration into the carcase) edge guides in place, with the guide's edge aligned perfectly to the offset (or original line if 3/8" offset is perfect). You will then be able to register the bottom side of the biscuit joiner against this guide, press down firmly to keep in from shifting when you power it on, power it on, then press inward and you'll have your biscuit slot.
Like I said earlier, if the built-in 3/8" offset from the base works well for your glue-up then all the referencing and alignment is pretty much quick and trivial. If you need an offset of more or less than 3/8" then you simply need to take the time to calculate the needed positive or negative offset, clamp your edge guide to match this offset, then make your cuts. Take a breath, take a minute or two to double-check your math and think things through and you should have no problems.
If you have a Woodcraft nearby, they have these
wonderful plastic shim sets that include 10ea of 1/32", 1/16", 1/8", and 1/4" shims. They are quite accurate and absoulutely wonderful for offsets in increments of 1/32" (you can stack shims to create any offset in even 1/32" increments). I use them to offset jigs, to gently step my router table fence in difficult woods, etc. and they are wonderful for these sorts of tasks. Use a little double-sided tape and stick them to the bottom of your biscuit joiner (or edge guide, depending on which needs offsetting) and you can establish a fixed offset for whatever offset your math suggests is optimal.
I hope this helps answer you question. It really is not a difficult biscuit joint to make, just a little bit nervewracking if you have never used your biscuit joiner in this manner.