Windows easily can be set up for dual boot. However, the only problem I see in your idea is a way to disable the 32bit boot disk when using the 64bit boot. I can't think of any way to do this.
You've got the 32bit system running so I'd activate it and just disconnect all current drives, connect your new drive, and load 64bit windows. When that's done and everything is updated and activated, re-connect your other drives. Then you can use BIOS boot selection (sometimes f12, f8, check your motherboard) to choose which one to boot. The reason for disconnecting all other drives is because Windows puts a recovery partition on one of the drives when it loads and doesn't always put it on the boot drive.
If you're trying to use the same key for both installs I don't think it will work but you could try it. Good luck.