In your situation I would not use Boot Camp at all. Boot Camp is designed to ease the installation of a secondary Windows install onto a Mac with a single hard disk. If you're dedicating a drive to the Windows install, all the EFI and GPT vs. MBR issues just plain go away. You do not need Boot Camp.
Blank the target disk via Disk Utility (not strictly necessary, but this makes sure you're pointing the Windows installer at the right disks/partitions). I simply tell Disk Utility to format the disk with a single partition, MBR partition table. This lets me format the partition FAT32 and then name it something like 'KILLME', which is visible in the disk selection stages of Windows install.
Install rEFIt to your primary OS disk. rEFIt is teh business for anyone booting >1 OS on a Mac. It's like the default Mac bootloader (option key), except it's more extensible and flexible. It'll boot most anything, too.
After installing rEFIt and verifying that it works as expected, simply put in the Windows 7 DVD. Reboot, and pick the big shiny round thing in rEFIt. The installer begins.
You could set up Vista or Win7 to boot natively into a GPT disk, using EFI directly instead of the BIOS module, but there really is *no* benefit to doing so. None at all.
Anyways, Boot Camp wizard is overkill and not really useful for what you are doing. You should be able to install another OS without using it at all, thanks to your config.
Behemoth - media server
Galactica - test lab server
Falling Outside the Normal Moral Constraints - MBP 15
Donnager - M4800 DTR
Rocinante - E5530 testing machine
Razorback - E6430 ultraportable