Hi again John -
I would wipe the HD first to remove any conflicting or factory code, then use booted Windows 7 install DVD Custom>Drive Options to create partition(s) as you wish, format before installing Windows 7 to first partition. SSD / HDD : Optimize for Windows Reinstallation
It will create Primary partitions with Windows 7 as the System partition.
A recommended method is to create an OS partition of 20-100 gb depending on HD size and number of programs, then a separate Data partition to place your User folders so they are in their own "vault." If Windows 7 ever won't startup or repair, you can reinstall or reimage the OS and programs to first partition and data will be waiting next door.
If you have enough space I'd create a backup partition on each HD to store a System image of the other HD's OS and date so you can easily reimage to a new HD in case of HD failure. This can also be done on an external HD.
I remember from another thread that you are planning to wisely boot separate HD's from the BIOS. Remember to unplug the other HD's during install, then set Windows 7 as first HD to boot in BIOS when you plug it back in, boot the other HD OS using one-time Boot menu key given on first screen.