Every program that will work in your current setup will work in the new one, because most programs will install into the x86 Programs File as 32 bit. So that's not a worry.
Sorry you paid so much for a disk for free Upgrade. We could have hooked you up with one here to use with the Product Key on your Upgrade COA sticker.
Adapt these steps to get a perfect reinstall:
Reinstalling Windows 7