Bartender

How we doing today Istan?
Have you tried anything else?
You're using an Ubuntu LiveCD, right?

I'd try again. With both dries plugged in.
Instead of going manual when you get to the partitioner, let ubuntu do a "Guided - use entire drive" but make sure that you -
1) Have your BIOS set up so that Windows HDD is master and the other one's slave
2) Make sure that the ubuntu installer sees sda as "NTFS" or media/windows or whatever it calls the Windows drive.
3) Make sure when you're at the "Guided - use entire disc" step that it's aimed at sdb, not sda. We do not want it to install to sda!!
4) At the last step before it starts to install Ubuntu gives you a little summary page. That summary page is important. In one little line that's not very obvious, it'll say something like
"GRUB will install to ..." and there will be a little tiny box saying "hd0". Change that to "hd1". Then let it install.
That should work. Windows (sda) will be left alone, the entire Ubuntu install will be on sdb, and you would choose by changing the boot order in BIOS or by using that key during boot that gives you the choice of bootable devices if your BIOS has that option.
If, in a few weeks, you decide that you want GRUB to install to the windows MBR, then you can re-install grub or just re-install Linux completely and let GRUB install to hd0.