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 you have an install disc).
An SSD isn't much more money, but a 120GB SSD (Samsung 840 recommended for $100) only has about 89GB after formatting and overprovisioning. If that's possible for you, you'd be amazed at the performance difference even if you only have a SATA1 connection. IDE HDD to SSD is simply amazing regardless of the rest of your hardware.
Cloning:
This can sometimes be problematic, but if a particular free program doesn't work, try a second one. Or, you can do a Backup, then Restore that backup (Acronis True Image or Windows Backup) from source drive to destination drive.
*I should add that there have been issues with cloning to the new Advanced Format hard drives (mostly worked but with issues); the only solution was to reinstall Windows from scratch.
I'm unaware if this issue exists with SSD's.