sure, you can ise both IDE connectors for optical drives, actually i would recommend it. if they are free.
but, you will probably need a disk to load the driver for you S-ata ports when you start the windows XP setup (press F6 to load other drivers) or something like that.
also, maybe you've disabled all of the onboard stuff you don't need in your Bios, (like onboard VGA, Audio, S-ata controllers, serial ports,...)
make sure you've enabled your S-ata ports
that's what I did, if you don't need it, disable it!