oynaz is right about needing to set it in the BIOS.
My computer first started with just a SATA drive, and it worked fine. I then moved 5 IDE drives into the computer to make this the new server (the motherboard has 3 IDE slots, the DVD drive occupies the first IDE master). When I did that I couldn't figure out why the hell the computer wouldn't boot; kept saying it didn't have a valid boot disk. I had to go into the BIOS options and manually tell it which of the 6 hard drives it's supposed to boot from.
After changing the BIOS settings, this computer works fine. The boot drive is SATA, the other 5 IDE drives are for random storage.
To answer your question: SATA is better. Not because it's faster, but because the cables are much smaller. Have you tried to work on a computer that has 6 IDE drives? It's horrible!
Another thing to consider is that SATA drives are getting much bigger and cheaper while IDE drives are basically at the end of their cycle. If you use up your IDE slots now, that leaves the SATA slots available for huge expansion when the time comes to get more hard drive space. If you use up your SATA slots, you can only upgrade with IDE drives in the future, or replace your existing SATA drives. It's sort of like asking whether you should buy 2x512mb memory sticks or 1x1gb; buying 2 sticks (like SATA) is faster, but leaving more slots open (using the IDE before SATA) allows more room for expansion in the future.