As suggested, unplug the Vista HD before installing Win7, then afterward you can replug Vista back in if you want to dual boot it, set Win7 as first HD to boot (after DVD drive) in BIOS boot order, or trigger Vista using the F-key given on first bootup screen for one-time boot menu.
However, while this is the cleanest way to dual boot with two HD's, you'll need to do a Repair Install (upgrade over itself) to get Win7 to accept Upgrade Version key since it won't see Vista when you boot the DVD and will reject the Upgrade key at first.
If you choose to let Windows configure the Dual Boot by keeping Vista plugged in during install, you won't have to do the repair install, but it will be harder to remove the Vista HD later, requiring marking Win7 active and running Startup Repair up to 3 separate times from the booted DVD or Repair CD.