When you say "one file on one sid and another on the other", you do know GoatTracker only exports a single SID tune. On top of that, the C65 isn't exactly a multi-tasking computer, so it's not like you can load up two "SIDplayer" programs and play a track on each.

If you're thinking about playing two different tunes at the same time, you're probably going to need to write a completely new application that allows you to specify two SID files, load them into memory and have an interrupt routine that processes each tune and updates the associated SID.

This isn't available "out of the box" (AFAIK), at least it's nothing supported by GoatTracker