You might get more people offering suggestions in the "Microsoft" bit but then this joint is still small enough it doesn't really matter.
You don't need me to tell you the obvious stuff like backups, etc, "just in case" but we've been managing our own exchange servers for years on Connect 2.3 onwards. We've ran Exchange 5.5, 2000, & 2003 and never had anything fall over because of it.
You should be aware that Exchange 2000 & 2003 do make heavy use of AD, but as you've got a fairly new install of CC3 I'm guessing you also have fairly highly spec servers so again this should not be an issue.
One immediate problem that springs to mind is that Exchange 2000 will not run on Windows 2003.
Windows NT can run Exchange 4 to 5.5
Windows 2000 can run Exchange 5.5, 2000, or 2003
Windows 2003 can run Exchange 2003.
Regards
Rob Moir
Brace yourself. For when I speak these words you may well suffer an attack of explosive amnesia.
For you see, the horrible secret is -