Should I get the 6Gbps HD and Motherboard?

A hard drive with a 6Gbit/sec SATA connection attached to a motherboard with a 6GBit/sec SATA connection won't perform ANY better than one using 3Gbit/sec SATA. The hard drives themselves are much slower than the connection is.

Only SSDs are getting close to the limits of 3Gbit/sec SATA. It will probably be the next generation of SSDs (or the one after that) where 6Gbit/sec SATA will actually make a difference.