One thing to note, some boards have additional SATA slots that are attached to a different 3rd party controller. Asmedia is one example, I think Marvell might be another. These are different from the Intel ports. The Intel ports are generally considered the better ones, and are the ones that you want to make sure you connect your boot drives too, as I havent heard that people are generally successful using the non-Intel SATA ports to boot from. Although they should work fine as regular SATA ports. Your manual should clearly label the different ones.
Just something to keep in mind, if your board has this kind of SATA set up (as mine does)