Just in case someone stumbles upon this discussion trying to get Time Machine and Boot Camp to share a second, internal hard drive, I did figure it out finally. Turns out, I was over thinking it and planning ahead for something I didn't need to worry about. Here's the order in which I did it.
1. Setup Time Machine on your second drive.
- Give it the full drive. No need to partition. (this is where I screwed up initially)
2. Run Boot Camp Assistant
- Select the Time Machine drive
- Select "Create a second partition for Windows" (if the drive is unpartitioned, this should be an available option)
- Decide how big you want the partition, etc...
3. Installing Windows: (I used windows 7)
- Choose to install to the "BOOTCAMP" partition.
- At this point Windows warned me that the partition wasn't formatted correctly, even though Boot Camp Assistant had done the partitioning. However, with the correct partition selected you can click on 'Advanced' and correctly format that partition for windows.
- Past that, everything worked as it should.
If this doesn't work for you, I don't know what the problem might be. This is the order in which I set everything up, and it worked flawlessly for me.
Someone above mentioned this being a terrible idea...I still have no idea why. As for me, this is the exact setup that I was wanting from the get-go, and I coudn't be happier with the final result.