Re: Sccm 2007 r2 sp2
SCCM 2007 R3 is now available depending on your licensing setup. Is this available to you? I believe it is if you are on Software Assurance.
With regards to Primary site placement, it would depend on the placement of the IT administrators. I have recently put in SCCM and went with 1 Primary site and the rest are going to be secondary. There are 7 physical locations, with 7 AD sites.
You would also need to consider the placement of Distribution Points as each site should ideally have one seeing that your Update and Software packages will be on them for distribution to clients.