Nikos,
This post is probably best suited for the Flex forum but to,
hopefully, help you out: when moving to a team environment, it is
very beneficial to get a repository setup. This could be based on
CVS, SVN, or the new craze Git (which is actually pretty nice
despite my tabbing it a crazy :). There are online options for this
(Codespaces, GitHub, GoogleCode) service: some free, some not.
Just as important, however, is that your team have an
understanding of how to use code repositories (checking out code,
committing, updating, etc.). I believe O'Reilly made one of their
books on SVN free, which could be very helpful (
http://svnbook.red-bean.com/).
You can install the appropriate SVN or Git plugin for Flex
Builder. The CVS plugin, I believe, is there by default but no one
seems to use CVS any more, preferring Subversion (SVN) or Git. The
Eclipse plugins, once understood by your team, will certainly help
your team keep project code organized and protected (from
overwrites, etc.).
As you are moving to a team environment, you may also want to
consider using one of the Flex frameworks (PureMVC, Cairngorm,
Mate, or Swiz -- the "big" 4, I suppose) as these frameworks are
well-suited for team development because of how they separate your
application into logical bits (model, view, controllers, etc.).
Just a thought...it helped me on a couple of team Flex
projects.