Basically setting up a hard drive is just:
1. Plugging it in
2. Partitioning it
3. Formatting it
4. Mounting it
I'll just assume you can handle the plugging in part. For partitioning, you can use a) text-based fdisk or parted, or b) Gparted, which has a very easy and nice looking GUI. If you use Gparted, it also does the formatting for you. If you rather do it over the command line, there's mkfs.ext3 and mke2fs that do the formatting. After formatting and partitioning you have /dev/sdb as the hard drive, /dev/sdb1 as the first partition, /dev/sdb2 as the second partition, and so forth... And you'd then mount a partition with "mount /dev/sdb1 /mnt/point". To do this automatically, you'd need to add the partitions to your /etc/fstab.