I have cut some short 3D pieces with FCP, mainly as technology demos, shot with 3DA1.

Now I need to do cut something that requires dissolves and other transitions. I am cutting Cineform files on a Mac in FCP.

What is the proper process for transitions?

Dissolves should be ok, but things like page peels, horizontal/vertical & circle wipes wouldn't really work, unless you did them per eye during an online style process...