I'm trying to insert an audio track I have on a CD, on the CD the track sounds fine, and after I rip the track (wave or mp3) it sounds clean, but after I import it into a track in X3 there are places where it sounds overamped, like somehow gain was added... does this even make sense?

MP3 encoding can cause clipping. If the track on the CD is highly compressed, this could be the problem. SONAR can import directly from CD as a .WAV. That would be preferable, anyway, and should solve the problem unless the issue is that you have another gain stage in the project or hardware bus strips somewhere that's causing clipping at the hardware out.