Your case and motherboard will work great together. No problems. I don't see the issue that you refer to with the PCIe slot and CPU socket. You're not confusing the south bridge heat sync with the CPU socket, are you? Either way, there is nothing to be concerned about.
Btw, that is a good inexpensive board. I'm putting together a budget build now with that board and a PHIIX4 965 and HD 6870.
thanks for the help i was looking at a msi micro motherboard when typing that. it was a bit smaller and had a different layout then the one posted