I would have thought the logical choice would be to use the SATA drive as the main HDD.
Anyway just to make doubly sure disconnect the SATA drive from your motherboard and boot with the Windows 7 DVD. The reason for this is that Windows 7 likes to create a small setup partition (approx 100mb) on the first free drive it comes across.
Now if Windows 7 sees your SATA drive first you may loose some of the contents.
Good advice from ulysses35, just unlpug the sata connector to the drive.
I would likewise question the use of the older IDE drive, if you are thinking about how XP needs sata drivers on floppy to install, W7 doesn't have that problem.