my suggestion is learn how to use maximizer and to start your clients through keyclone.
Create the maximizer regions as overlapping if you want ( I do ) and setup the PIP so you can bring any client up to your main region as needed.

I think the so called problem with overlapping regions in Vista has to do with the one of the advanced areo features ... transparency or something like that. Just turn if off.
I'll try to find a link to it