In BIOS, under Boot Order, do you still have IDE-0 booting before SCSI or RAID devices? (usually you would want boot order to be something like: CD-ROM, Floppy, IDE-0, etc)
Your original IDE HD's jumpers should be restored to whatever they were when things worked (whether that was CS [cable select] or Master)
I don't know about any jumpers on true SATA drives, so can't offer any advice here.
Does your SATA controller card support RAID-0 or RAID-1? If not, they you'll just have three drives (IDE, SATA, SATA)