FlexBuilder 2 works fine with CVS, we do it all the time,
it's just a big Eclipse IDE.
Buuuuut.... unless you're in a rush to get your GUI design
done in Flex (possible) you may want to do parallel development in
both Flex and your server side language (Java etc), with one person
using FB and the other working on other aspects of your
application. Of course that's assuming there is a significant
"other side" to your app. It's a little easier, few (if any)
conflicts to worry about developing that way.