Another way you can do it is to leave your hard disks the way they are and install Ubuntu on your second hard disk and install GRUB to your second hard disk's MBR.
If you do that Ubuntu won't boot.
Not unless you press your F8 key or F12 during boot-up or whatever key it is that brings up a boot menu from your computer's BIOS, (if your computer's BIOS has that feature, most do), and select your second hard disk.
Then Ubuntu will boot.
To direct GRUB to install in a non-first MBR or in a partition (boot sector) or wherever you want, you need the Ubuntu 'Alternate' Installation CD. See the following link for details, Ubuntu Hardy Heron Two Disc Multi Boot
The Ubuntu 'Desktop' Live/Install CD may be able to do it too. You can try by hitting the 'Advanced' tab in step 7 of 7 of the install, and type in (hd1), on the line for where to install GRUB to.
See the following link for details,Hardy Heron Beta / Gutsy Gibbon Dual Boot Installation A
Actually, it would be okay to install GRUB to both or all hard disk's MBRs.
GRUB is clean and safe, whereas Windows is subject to viruses which infect the MBR and boot sector. Windows will boot okay from any boot manager in the MBR, but it's boot sector is vital.
GRUB has far more features and capabilities than any other boot manager or loader.
You could make a dedicated GRUB partition on all of your hard disks and install GRUB to MBR in all of them and you'll never have any problems booting under any circumstances, if you know how to use GRUB. How to make a dedicated GRUB partition