I've used FCP to edit in 3D, it's not that easy. What we've done is to set up 2 monitors and stereo projectors with a Matrox Dual Head 2 Go to create side by side edits. the edits are then sent to Motion or AE for final compositing.
We're planning on trying out the 2 new plugins from Cineform and Noise Industries to see if they improve our workflow.
If you're in NY, you can swing by our shop and see how we do it. Email me off list at arniepix @ arniepix (dot) com.
Arnie
Post production is
not an afterthought!
http://www.arniepix.com/