Disregard the first two diagrams. The third one is what you want and wire the input from source (house) to the input of the timer. The load side of the timer gets wired to the Pool pilot terminals 1&2. Make sure the jumpers are done according to the instructions. Don't forget the grounds. Look over the connections on the terminal striip, see if you understand what is directed in the instructions before you do anything. If you want I'll try and get a picture of the terminal strip connections tommorrow night. My timer is mounted next to the PoolPilot, best place for it.
Don't get discouraged, the setup works great once you get it going.