How do you have 2 Master HDD's? That doesn't work. Is one SATA and one IDE you meant?
Umm...I would install Windows first on the primary HD if that's what you want as your primary OS. Then just freshly install Ubuntu on the second HD. It should prompt you automatically upon boot-up.
Okay so, I would make sure you don't need a Master/Slave setup. I've actually run this setup also with same OS's and never had a problem when installing Ubuntu on a 2nd HDD after I had XP on my first one for a while.