Zach, since you're looking at plug cutters, I thought I'd share a couple of things I've found useful about using plugs.
When you are cutting tapered plugs, don't make them a whole lot taller than the depth of the holes they are going into. If they are too tall, they'll be too small to fit in the holes tightly.
The plugs should be installed with their grain aligned to the grain of the board they are going into. To make that easier, I use a trick I learned from an old boat builder. I rip strips slightly wider than the diameter of the plugs and cut the plugs down the strip. I do this on a drill press and set the depth stop so I don't cut the plugs free.
When it's time to insert the plugs invert the stick, offer the end plug up to the hole, and drive it in with a hammer. It breaks free of the stick and the stick makes it easy to get the grain aligned.
Leaving them on the stick also means you don't get your fingers in the stuff you're using to seat the plugs.
Another boat builder's trick when setting plugs is to use the varnish or whatever finish they will be using on the piece to seat the plugs. This has three benefits. Since the plugs aren't structural, the varnish is plenty strong enough to retain the plugs. There's no risk of a glue line that won't take finish, and if the plugs are covering screws that may some day need to be removed, they can be extracted without damaging the surrounding wood. That means a plug of the same size can go back in the hole when the piece is reassembled.