Here's a link to an article that may be useful:
http://www-128.ibm.com/developerworks/lotus/library/notes-eclipse/
1) I don't work in multi-developer environment as far as Domino with Java goes. Eclipse does support CVS so that seems like it would be the way to go.
2) For debugging. Writing your own classes for exceptions and logging is extremely helpful for server-side debugging. For notes client, you can have your exception and logging classes write to System.out so you can see the output in the Java debug window. For server side, you can have the exception and log classes write to Notes document. You can also write to System.out which will end up in the Notes Log, but it can be hard to find your output in the Notes log if you have a lot of stuff running on your server. Supposedly, there is a server-side debugger available for Domino 7, but I haven't tried it.