BootCamp is simply a partition manager; nothing more; therefore if you have a second drive, just insert your Windows installation disk at boot up, hold option, select it and install. When you get the part that asks you which disk to install it on, just select the second disk.
IF you don't want to the entire second disk for Windows, you can partition it beforehand in Disk Utility as needed before proceeding with the installation. Boot Camp Assistant will only let your partition your primary booting disk, so the only way to partition the second drive is to use Disk Utility.
Just be cautious not to accidentally install over your OS X installation.
If you need anything else, feel free to ask.
Regards.