Lion, Ubuntu, Bootcamp, Dual HDD, HELP!?

I have a Mid 2011 13" MBP that I use for work, it currently has a little 320GB HDD in it from Apple. I'll be ordering two 1TB 9.5mm Seagate HDD from Newegg.ca, and the Optibay kit to replace the factory optical drive with a second hard drive.

Now I have a Ubuntu desktop PC but it's getting old and as more and more flash insistant websites are popping up it just doesn't have enough power to keep up. Rather then buying a new CPU, GPU, and more RAM couldn't hurt, I would rather just get rid of it and use my MBP as my desktop computer while dual booting Ubuntu on it.

The big question though is whether or not I can run Ubuntu as my main OS on one hard drive, and then have Lion (Mountain Lion soon enough) as the main OS on the second hard drive?

This giving me a 1TB drive for my every day home computing needs with Ubuntu as well as a 1TB drive for OS X when I need to do work. Then I can get rid of my bulky desktop Ubuntu PC and replace it with the Henge Dock for my Mid 2011 MBP.

One computer, two work stations, two separate applications. I really hope Bootcamp can work like this, I've never used it before but as far as I know, it just partitions the hard drive, changes it from HFS+ to NTFS and installs windows. But I would like to use Bootcamp to install Ubuntu on one hard drive and keep OS X on another hard drive.

Does anyone know if this will work?
I would like to be sure before I spend 300 bucks on hard drives and the Optibay kit