Given the setup with two 500GB hard disks, I recommend you look into Logical Volume Management (LVM). This adds to the complexity of setup, and is something new to learn, but it simplifies matters in the long run. With LVM, you add one or more partitions or disks (called physical volumes in this system) to a volume group, from which you allocate logical volumes, which hold filesystems in much the way that partitions do in simpler configurations. The advantage is that logical volumes are treated like files in a filesystem, so they can be manipulated much more flexibly than can partitions. In your case, a big point is that a logical volume can be bigger than either of your disks. In your current setup, if you use regular partitions, you'll need to split your user space across two disks. Ubuntu itself doesn't need even 1/10th the capacity of one of your disks -- perhaps 30GB for Ubuntu's root (/) plus a generous swap partition. That leaves about 470GB on one disk and the entirety of the second disk free. In a conventional partitioning system, that means two mount points (/home and somewhere else), and you'll need to manually manage what files goes where. With LVM, though, a logical volume can span multiple hard disks, so you can have a 970GB /home and not worry about filling up your main /home directory vs. wherever you mount your additional space.
LVM also simplifies adding space. If you add a third disk, you can add it to the volume group and then extend any or all of your logical volumes to make use of that new space. LVM obviates the need to move partitions, and expanding them becomes safer.
That said, Ubuntu's desktop edition doesn't have good LVM support, so you'll need to jump through some extra hoops to set this up. The page to which I linked earlier covers how to do this, so read it to decide if you're comfortable with those extra actions. LVM's extra redirection can also make it harder to recover your filesystem if something bad happens at a low level, like if the LVM data are damaged.
