If you do the install from the downloaded files and not from a bootable DVD, at least move them to another partition, or even copy them to a normal DVD and run it from within Vista. If you don't want to upgrade from Vista, which most folks don't suggest, you will be doing a custom install. I believe that will remove Vista from your system, except for the old files carried over for archive purposes, and install a fresh OS. If you want more, on the lower right of the partitions screen is a Disk Options button for doing other things.
This all is based on you not having an Upgrade version of Windows 7. If you do, I would not recommend using the Disk Options.