My system has an IDE and a SATA drive. Windows XP and Ubuntu 9.1 are installed
on the IDE drive, and I have Ubuntu 10.04 on the SATA drive. My computer selects
the IDE drive as HDA-0 (C:) by default, but by going into Setup on boot, I can
select whichever hard drive I want as the default boot drive. Both drives on my
system have GRUB installed.

When dual booting with one hard drive, Windows should always be installed first,
because it overwrites the boot sector.

When using two drives, it may be easier to disconnect the drive you do not want
to install Ubuntu on. After the installation is complete, shut down, reconnect
the other drive and after booting, open a terminal and enter "sudo update-grub".
This will rewrite GRUB to inslude the other drive.