My experience with external version control in VAJ 3.5 is "Don't Do It!" I had a sizable redbook about it, and I never got it to work. Granted, it was PVCS and not CVS, but the interfaces were largely the same. It's far easier, more cost effective, and less annoying to use the built-in versioning features and make sure you have a backed-up repository. The best option though by far is to step up to WSAD or Eclipse. =)
"Write beautiful code; then profile that beautiful code and make little bits of it uglier but faster." --The JavaPerformanceTuning.com team, Newsletter 039.