SATA, because youll be using youre OS constantly, which means your OS will work a lot better. That's just one mans opinion. Plus I believe the Raptor has a lot better features like NQC, I think it is which basically helps your HDD to be more efficient.
Personally I would use it for my OS and other apps I use on a daily basis. FASTER is BETTER. I would probably use the IDE for secondary storage and backup.