You probably want to relocate your /var and /usr to the extra drive. To do this, you'll need to make two partitions (usually ext3 or reiserfs formats, whichever your distro prefers) on the drive, mount them under /mnt (as will be done by default) and then copy the contents of your current /usr and /var to the respective new space.
If your distribution also has a large /opt directory - check by doing:
you can similarly relocate that directory.
Then you'll need to change your /etc/fstab to mount the new partitions as /var and /usr at the next reboot (or you could remount everything without reboot, but a reboot is probably easiest).
Eventually, once you know everything is working, you'll want to umount /var and /usr briefly so you can delete the contents from the old space.