To comment on your 2nd post:
Installing SATA II 3.0Gbps drive to a SATA III 6.0Gbps mobo port will not change anything about the hard drive, it'll still go at SATA II speeds.
However, be aware that some drives don't even run on SATA III ports, even thought they should be backwards compatible.
And, hard drives don't even come close to flood the SATA II bandwidth. My drives, 2 in RAID 0 only get 150MBps, and my single gets 110MBps. That's approx. 1/3 the bandwidth. (Note my 150MBps is in RAID 0, so I should have double 3.0Gbps, but I don't.)
To comment on your first post:
I'll have to check the drive information.
I found that the WD5000AAKS is a Western Digital Caviar Blue 500GB 7200 RPM 16MB Cache SATA 3.0Gb/s 3.5" Internal Hard Drive. Blue is better than Green, not a good as Black.
I found that the WD5000ABYS is a Western Digital RE2 500GB 7200 RPM 16MB Cache SATA 3.0Gb/s 3.5" Hard Drive. Now, I think that the RE means RAID Enabled, recommend for RAID setup. And WD is very picky about this. They will not support non-RAID drives in a RAID array.
Now, they are the same size, cache, and RPM. So I think a RAID 0 will work fine. The only thing I'd check is read/write speed for them. If not equal, the array will be dropped to match the lowest drive rate.
Good Luck.