I'm not a Premiere user, nor have I made any stereoscopic movies, but I'm just about to start experimenting in that realm. There are really two possibilities here:

1) take the left- and right-channel videos into After Effects, sync them up, and export each take as one big, wide video file that you can then edit with in Premiere. This takes more work up front and is a less flexible option, but it may be easier on your graphics card if you have an older computer.

2) use multiclips (that's a Final Cut term, but I would assume that Premiere has a similar functionality) or nested sequences to synchronize the clips and edit directly in Premiere. The advantage of this is flexibility: when you're done editing, with very little additional work you can output in any number of formats: separate video files for each channel, crossed-eye stereo, divergent-view stereo, red/blue anaglyph, whatever.

Personally, when I do eventually try this out I plan on going with option #2, just to keep my options open.

-----------------
Andrew Gingerich
Exploding Goldfish Films
Check out my blog at http://www.exgfilms.com
and my reel at http://portfolio.exgfilms.com