I've done a couple stereo tests with AE, and I found it really cumbersome because the software itself lacks built-in stereo support. Nuke might be a better option, because stereo support is built-in to the application.
Check out Chris Keller's awesome stereoscopic scripts for After Effects. I've used them a few times. The workflow is still a bit clunky because of AE's limitations, but these scripts are an incredibly well thought-out workaround for this, and they will save you hours and hours of work.
You might find some more information on the Stereoscopic 3D forum here.
I'll also point out a couple threads that helped me:
Principal & Designer at Keen Live
Motion Graphics, Widescreen Events, Presentation Design, and Consulting RenderBreak Blog - What I'm thinking when my workstation's thinking
Creative Cow Forum Host: Live & Stage Events