you should not fear cloning hard drives (ghosting) in the least bit! cloning is a god send and easy to do if you have data that you want to keep protected!
Imaging is another great tool
as for spped diff in sata and IDE the peformance improvement is very slight, not worth chasing for the most part
the REAL advantage that I love about Sata drives is the thin data cable which improves air flow in the case big time ! that improved air flow is
worth chasing and eliminating IDE drives in computer systems
Right now for the most part, hard drive speed is the slowest thing in the computer system, although keeping your OS on a seperate small partition and your programs and data on another partition or seperate drive does speed things up a "wisker" I dont think the gains are worth much time investment, if any ? It more of a "conversation" improvement than a real life performance boost.
I know some fellas that keep all their programs and data stored on a seperate drive, then when (not if) windows crashes / they dont have to mess with the programs and data, they are all there to be saved.
however cloning and imaging have devoured that "theory" IMHO
if you have any other questions, fire away
BTW it may help if you post your full system specs, any performance boost that may be achieved by the hard drive set-up you proposed would best be had with a newer system, not hardly at all on system two or three years old