Plug in both harddrives, just install windows to the IDE drive, and it will become your master drive. The sata will then sit idly by as a storage drive.
It would probably help to set the IDE channel boot priority above that of the sata channel in the BIOS as well just for added measure.
satas don't have any jumper settings for master slave either, just thought i'd toss that out there. normally just jumpers for sata 1, or sata 2 setting