Are you talking about taking a track from preproduction to production? There are many ways to do this. Here's what I normally do. You'll want to record each instrument individually so that you can dynamically process, eq and effect the instrument without affecting the whole mix. You can apply processing while tracking or while mixing down or both depending on what sound you're trying to get. Do this for each instrument track and if possible separate the drums into separate tracks (kick, snare, overheads).
Now in order to have everything line up you'll need to use MIDI to synchronize everything. You can do this with the Roland/Boss-type recording units (VS and BR-8s). I personally use Logic for this which I find a lot easier than the BR-8 I was using prior.
I can give you more specifics on this is necessary but I hope this helps as a starting point.
Stray