when you get any overlap just drag the end or beginning of one of the audio tracks to remove most of the overlap but making sure that you're not cutting off any of the audio from both sources.The overlapping is to ensure smooth transition. Just play about with everything as i find this is the best way to learn Vegas.
To export the file just goto "render" and select AC3 as your output. Vegas has a AC3 preset for both 5.1 and stereo