Split wife's family from mine

I just installed my shinny new FTM2012. As a big computer klutz, I have a great fear of doing something wrong. When I started with ancestry.com over two years ago, I had no idea my tree would grow so large, 6000+ now. I'm really hooked.
I want to make sure I do this the correct/best way.

I'd like to split my second wife's large family from mine. I want to name that tree Wallace-Starnes, her parents. I'm from the north, she from the south. There are no past connections.
I guess I'll change my tree from Burt to Burt-Gross for my parents.
Since it is a large tree, should I/could I do the split in ancestry.com before I upload it to FTM2012? The main thing is to not mess up all the work I've done. What ever you suggest, please give me the exact way to do it?

Thanks

Roger Burt