supposing you just go through the play-and-record route, which is definitely an option, here's a trick. if you are going to be using a computer with a multitrack program that can handle many tracks, I'd do this:
-program your song, and have a 4 or 8 count click during the intro.
-when you go to record it, leave the click on, and turn everything off except the snare and record that.
-now record the bass drum with everything else but the intro click off
-go on down the line of the drum kit, always keeping the intro click.
-line up the beginning clicks in the computer so they are all on time
-now you can control each drum sound for the mix, as far as panning and level goes. if you assume your drum mix is a done deal, chances are the bass or snare will need tweaking later and if it's stuck, it's stuck.