If you're going to keep having two drives, I recommend that you put them to good use: replicate all your important files on the two drives. It's called software RAID1; Linux supports this reliably and efficiently. That means your disk partitions would look like this:
first disk second disk
sda1 md0 sdb1 md0
sda2 swap sdb2 swap
sda3 /LARGE sdb3 /MORE
md0 is a RAID1 volume;
sdb1 automatically contain identical data. That way, if one of your disks fails, you don't lose any important files, and you can continue working with your computer until you get the failed disk replaced.
md0 would contain two partitions:
/ (for the operating system) and
/home (for your important data — stuff that you created, as opposed to stuff that you downloaded or ripped or compiled from somewhere). I like to have 20GB for the OS (I install a lot more programs than the average user). It's hard to say how large
/home should be: it depends what data you (plan to) have that you consider important.
The Ubuntu installer can create RAID1 volumes, but you need the “alternate” or “server” installer, not the default “desktop” installer.