Directions for .it and .s3m formats!!!
If you choose to use .it or .s3m files, you will have maximum control over playback, enabling you to change MANY things at runtime. It is easy to loop correctly, to mute individual channels, etc. This can be done with bass.dll which is free for non-commercial use.http://www.un4seen.com/bass.html
For example, you could start with drum channels or bass or melody muted until a significant event occurs in the game. For example, if an .it was being in Super Mario and you wanted to amp up the game when Mario collects a star, you could un-mute the bass and drums tracks while the star is in effect. Then as star-power time was running out, you could fade the two tracks.
Modplug Tracker (MPT) is probably the best and simplest way to play around with the songs:http://sourceforge.net/projects/modplug/
You just have to click on the heading/title/top of a track to mute it in Modplug Tracker.