If can get your computer to run on the hard drive that you want your OS installed on with the second hard drive installed in your computer. Go to "Start", right click on "My Computer", "Manage", "Storage", "Disc Management (Local)", right click on the hard drive you want formatted and "Format". Follow the instructions... you'll probably want a basic disc NTFS.
If you can't
get your computer to start with both hard drives installed, get an external hard drive enclosure from pretty much any computer place. Make sure that it's a 3.5".
Put your drive in there and plug the enclosure in via USB after computer start up. Follow the instructions from above. After formating your hard drive, replace inside your computer and make sure it's enabled in the BIOS settings.
When buying your external hard drive enclosure make sure that it supports your hard drive type (IDE or SATA or both)or you won't have the right connector cables, and that it supports your hard drive size, or you won't be able to format the entire drive. You can find good hard drive enclosures for about $20, and even cheaper when on sale. Here's one to look at.
Let me know how it goes.