As per Shaun,
You often have the Boot Order split (not always).
First, you choose what GENERAL order. I don't know if it will show IDE or SATA, it may simply show HARD DRIVE. So you might end up choosing:
1. DVD
2. Hard Drive
3. Nothing
Then, under order for "Hard Drives" you might see both your IDE and SATA drives listed. Again, it depends on the BIOS how this information is presented.
So you choose whichever drive you intend to boot from.
Other:
I recommend you replace the IDE drive. It's probably old and prone to failure, not to mention SLOW. For $70 you can find a 500GB or 1TB SATA drive. You could then CLONE the IDE to SATA (once you solve your boot problem) or possibly reinstall Windows after making suitable preparations (if...