Actually, I think I figured it out. Multi-tracking probably was over-complicating it. I started a new audio file, then copied and pasted each track into it, with the non-active track (side, essentially) turned off. When pasting the first one, it pastes to both right and left, but when you past the second one, it only pastes over that side.
What I did was turn off the right channel, then paste track 2 (from the right mic) into the left channel. I then turned that off, and pasted track 1 (the left mic) into the right channel. That seems to have done the trick. (mics were in XY configuration, hence the side change)