Band-in-a-Box has 2 tracks that you can use for your own purposes (bass lines etc.). These are the Melody and Soloist tracks (note: MIDI only, not audio). In addition, you can use any track for your own purposes if you freeze it (right click on the the 'Bass" at the top of the screen and you can freeze the bass track. Then notes entered on the bass track will be yours. You can do that after BB has generated a track, in case you just want to tweak it.

If you want to do a lot of your own tracks, I would recommend booting up RealBand, you can record 48 tracks (audio and MIDI) as well as generating BB tracks from that. It is included with Band-in-a-Box.

There is a RealBand getting started video http://64.40.109.185/pgmusic/wmv/RealBand.wmv

Have Fun!
Peter Gannon
PG Music Inc.