No problem. I used Cool Edit to record, edit, track, and denoise recordings I made from my vinyl collection. It's actually Cool Edit Pro that was a multitrack recording application, which is now Adobe Audition.

When I hit a burn out point with guitar, I'll take a closer look at Reaper in case it does something I can't in Adobe Audition.

Regarding recording with they Mustang II amp, here's a link that might help:
http://www.tdpri.com/forum/amp-central-station/264435-fender-mustang-usb-recording.html

The only drawback is you can't playback into the amp - so you can't play your backing track through your amp. Not sure how that would work with distortion and stuff anyway.

So you would have to record into your PC using your amp while playing your backing track from another source. Then, load both your backing track and recorded guitar track into something like Adobe Audition or Reaper, sync them up, set levels, etc. etc.