It you really want to be sure the easiest thing to do is just unplug the old standard HD. Then when you reinstall Vista it will only see the SSD. After he install and update plug in your old standard HD and the system will see it.
I'm sorry I didn't give the whole story. The original set up was using Vista 32. The original set-up also had some data corruption due to a virus. The plan was/is to wipe disk the original drive and make it the location for data and programs, and use the ssd to make the upgrade to vista 64.