I'll just continue this post as I figure things out just in case there's anyone else out there with this problem. So now I've figured out how to mark the partition as inactive, however there may be a boot loader or something on it as it's still labeled as a "system" partition. I'm going to manually unplug the drive to see if it boots without it plugged in, if so, then it's okay to wipe it. However, it won't allow me to wipe it unless I use a Linux live cd or something. =\ Windows can be frustrating. Here is the link I found on how to mark the partition as inactive.
http://www.sevenforums.com/tutorials/197157-partition-mark-inactive.html