There's two possibilities.

1) Just play a different soundtrack. Easiest way to do this is just put a small stereo or iPod player next to your computer and turn the game's music setting down to zero. Doesn't have to be in the game at all.

2) Play different incidental music based on what's going on. Sins music is sorted according to the race you're playing and the level of action and activity at whatever planet you're viewing. From looking at the files, there are about 60 different pieces of music that are included. If you can convert your own music to the Sins .ogg format (not sure if this is possible - maybe someone else can comment?), you can just rename your own tunes to the ones in that directory as a mod.

As an aside, I happen to greatly like Sins' "vanilla" music. There's enough variety that it never became boring to me.

-- Retro

OGG is a free format, so that should be pretty simple to do. For those not disinclined to a bit more effort, you can add the new tracks to the music list and specify the mood triggers, etc, as with the base tracks.