The place to start is the Unity 4.0(3) networking guide which can be found here:
http://www.cisco.com/en/US/products/sw/voicesw/ps2237/products_installation_and_configuration_guide_book09186a00801ba396.html
That will give you an idea of the range of options you have at your disposal.
The best options would be to have both Exchange servers in the same directory (you didn't give us much details on your topology - on vs. off box doesn't have much bearing on the question at hand here).
I'd read through the doc and get a feeel for how this works in general and then come back with more specific follow up questions.
