When setting up the dual boot the 32bit edition's primary was made the default boot partition in the process! You can't reformat the boot partition while being in the OS that loads from it without seeing that type of message come up.
The fast and easy solution would be booting from the Vista 64bit disk you used and using the reformat option while booted live from the Vista dvd. The need to see the 64bit BCD rebuilt will then be the next step since the present installation will then no longer boot up.
1)You can nuke the 32bit primary entirely leaving a vacant space and move the 64bit primary to the front to see that expanded with a need to rebuild.
2)Or you can see a clean install on the first with a reformat of the second in mind to avoid two copies of the 64bit edition. That will leave a second for storage available.
3)The third option is simply deletion of both for a brand new single large primary using up the entire drive.
You can opt the first to leave the present intact but spend time moving it forward to expand after and follow the rebuild BCD information outlined at How to use the Bootrec.exe tool in the Windows Recovery Environment to troubleshoot and repair startup issues in Windows Vista
The other option available for seeing that problem solved in found in the sticky on performing a repair install of Vista. Repair Install For Vista