There are several things you can do, and it depends on how much you want to change.
data\audio\music contains all the music in the game in wav file format. If you like, you can simply swap out some of the wav files for your own.
If you want a greater degree of control, you will need to update data\audio\music.ini or (I think) the data\universe\universe.ini, which contains music settings for each of the systems. If the music setting for the system is not there, it will be in each of the specific system.ini files in the subdirs off data\universe\systems.