In my navy time I have flaked out more ropes than had hot dinner's. As Charley Noble said it is run up and down the deck, you can do it with cable as well, but the most common reason for flaking a rope was to pay it out etc, to take a ship in tow. Each time it is layed out the next flake is laid over the previous one, so when it payed out it does not tangle. If you look at a cadburys flake bar it is similar.

Cobble.