Plug in only the target HD to the first port, boot the Windows 7 DVD, select Custom Install then when the Drives Selection screen shows the HD, click on it, delete all partitions, click Next and it will create and format your partition and begin the install.
There is no worry about it being C drive because Windows 7 willl alway see itself as C when installed correctly from booted DVD.
If there is an install failure, post back the exact error message and at what step it happened in this tutorial which shows the illustrated steps:
Clean Install Windows 7