This used to be done using NetInfo Manager, but that's not part of Leopard. I assume you're running Leopard since you've just bought the Mac Pro.
In Leopard, location of home directory is controlled by System Preferences -> Accounts. Select the user in the list and control-click to bring up "Advanced Options..."
Choose the directory on your second drive which corresponds to the one in "Users" that you copied. Don't change any of the other things.
By the way, it's always a good idea to have an extra admin account with home directory on the boot drive. That way, if something goes wrong with your second drive, you can still log in. As the admin, you can correct problems with your "primary" or "main" account.