I simply told the app to look for .m4p files and back 'em up. This might catch some files that aren't from iTunes, but that's ok.
If you are very clever you can just browse to your iTunes library and it will search only within that folder. I, clearly, am not that clever.
Mozy can be scheduled in two ways: automatically or with a set schedule.
If you choose automatically Mozy will backup your files when your Mac isn't in use (by looking at how busy your Mac is and how long it has been since someone used it).
Mozy tried to play nice with your available bandwidth (which is more than Time Machine and a Time Capsule do). You can set it to throttle in this preference window. By default it only uses 1.0 MBits/sec.