I use external drives in boxes or bays.

I have two 8-bay enclosures with 1TB drives in each bay as my main setup along with a 4-bay enclosure with 1TB drives. In addition to a smaller system drive, I've got 3x2TB drives internal in my main machine and the same setup in my back up machine which is a clone of the main.

I use Carbon Copy Cloner to do my backups.