I just did this over the summer with a win2k to vista upgrade. Just install vista on the new hd with the old one unplugged. Then, as old hippie said, just make sure your old hd is not in the boot sequence and you should be good to go. I vaguely remember vista complaining about another installation of windows...but I think you should be fine
Check your BIOS. There will likely be 2 things to look for in relation to booting. First, there will be an option to boot from HDD, CD-ROM, floppy, etc. Second, when you have multiple hdd's you'll need to set which one is the boot drive. Take a look at the model numbers of your drives and choose the newer one to boot from. It should boot into your new setup and your old hdd will be E: or F: or some other letter.
for me, it was as easy as opening up the bios (f1? del? depends on who made your bios), looking for the menu item that edited the boot sequence, removing all other drives/peripherals from that boot seq and leaving only the HD of choice. (sorry if that's vague)
...this was my ghetto way of dual booting linux and vista, with each installed on a different HD.