This was one of the articles I'd seen discussing NCQ and its advantages/drawbacks:
Frankly, I had gone for the SATA drive after my initial repair install on my existing IDE drives was a failure. I assumed that the mobo really wanted me to use SATA drives.
But with these issues, I'm starting to reconsider the setup. The reason I have so many drives is because I use the machine as my music recording setup. It's ideal to have separate drives for the OS, paging file, audio samples, applications, and song files. So perhaps going back to square one and using that SATA drive for song files (which are big and are constantly being written and overwritten) instead of wasting it on the OS is my best shot.
For now, I'll stick with trying to get the OS installed on the SATA drive as I've been trying to do, if only to finally solve this problem, for me and anyone else who checks this topic.