I've been doing that also. When I open up FCP both projects open up together. So after a while I got tired of this and I dragged one sequence from one project into the other.
I've done that a few times. I've also dragged most of the clips from one project and saved them in other projects as the movie has more than one version.
It's real messy and I wish I'd followed a clear procedure. As you may imagine I've done all this without studying the manuals :-)
But one time I also created different bins for different versions and this seems to work the best so far, because I can open the bin when I need it and close it (it collapses into one item) and that's not so bad. This way I open only one project and work out of one timeline, instead of two or three. Working with multiple timelines also entails clicking between the different browsers.