There is no in place upgrade from EX 2003 to 2007. I purchased a new server with WS2003 R2 64 bit and installed Ex 2k7 and installed SP1 into the same OU as 2k3. Followed migration procedures from msexchange.org Transitioning from Exchange 2000/2003 to Exchange Server 2007 (Part 1)
I then changed the mapi profile on my BES 4.1.4 server to connect to the 2k7sp1 server. I have not tested the OOO from the BB, though when I set it from Outlook 2k3 it seems to work fine. I will test it again though. I have only been away from the office a couple of times.