Just got my new build up and running. Asus m4a89gtd pro(890 GX Chipset) with a WD 6 Gb/s hard drive. If I put my old 3 Gb/s hard drive on the same board will both drives run at 3 Gb/s? Or will they both run at their own speed?
You can mix both drive types with no problems. SATA is designed to be downwardly compatible - the drive negotiates with the port to select the highest speed supported by both ends.
Whether you use a 3Gbit/sec or a 6Gbit/sec port is irrelevant for hard drives as the drives themselves are much slower than either. It's only a few of the very high-end SSDs that can actually exceed 3Gbits/sec.