I would recommend learning about Subversion (which is a lot like CVS, only a little more modern): http://subversion.tigris.org
There is a plugin for Flex Builder (Eclipse) that makes using Subversion quite easy: http://subclipse.tigris.org
There is definitely a learning curve to setting up and using a full-fledged source control system such as Subversion. But it is well worth it (and some would argue an absolute necessity). You can also find hosted Subversion providers, which would reduce your setup time. Take the leap.
Let me know if you have more questions...
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Yeah, some sort of versioning system is the way to go. There will always be some setup though. Which one you choose is a matter of preference. I personally use GIT.
Thanks. Both options see workable. I will likely go with subversion since it has a larger following. What server sertup is required in order to use subversion?