Ok thats a ton of questions! But, i understand why. The manual STINKS to put it mildly.
Lets tackle the 2 transformers first then go back to the pump.
One point first is how the relays work. It's actually pretty straightforward. Each relay is really just a switch thats put between the power from a breaker and the item it controls. The other function is as a way to distribute power. Each relay has 2 lines in (one for 120v, the other for the second hot leg if 240) and 2 loads out if you want to use the relay as a switch.
1) X-former that run the ET box.
Ok, this can be wired a couple different ways. One way is to wire it up on the breaker for the pump. This is generally 240. The black wire and yellow wire are run into the 2 "line in" terminals on the pump relay (labeled "F") (purple wire is capped off). Of course, the 2 "line in" terminals have the 2 hots from the 240 breaker ties in there as well. Really, you could wire nut the 2 hot leads from the breaker to the 2 hot leads from the X-former and a pig to go under the terminal screws. It would be the same if you didnt want to stuff multiple wires under those little screw terminals. This set-up powers the box itself and stays on even if the pump is turned off at the "F" button since its wired into the line in terminal. This way to wire it is fine, but does have a drawback. If you turn off the breaker for the pump, the box goes dead. This means that any other function such as lights, etc thats run by the ET will not work. The better way to power the box, IMO, is to hook the transformer up to a dedicated 15 amp, single pole breaker. Wire it up with black to breaker, purple to neutral bus, and cap the yellow. The disadvantage is that it takes up a breaker slot, but to me, this is the best way to wire the ET box. Each relay doesnt really need a dedicated breaker. You can run more than one off of a single breaker if you dont exceed the capacity for the circuit. Think of a single 20 amp, 120 volt breaker in your house that powers a number of plugs and lights. You would tie in a single 20 amp, 120 volt breaker into say AUX2, and put a jumper wire from line 1 over to line in 1 on the AUX 3 relay. That way, AUX 2 and 3 would be powered off of a single 20 amp breaker with ~2400 watts of power between them. More than enough to run a pool light, etc between them. But I digress.
2) Intellichlor transformer.
This one is best wired up to the 240 breaker that runs the pump. The box comes with the 240 wired up (you have to change the configuration as shown on the inside of the box to go to 120 volts). Wire up the pump breaker with both hot wires from the breaker to "line 1 and line 2" on the pump relay. Now, put the blue wire under one "line in" terminal, and the brown wire to the other "line in" terminal. The IC-40 will have power all the time, powered from the same breaker as the pump. However, even with the pump off, the IC 40 will still have power. Thats ok. When the pump is off, the IC-40 will not function since the flow switch on the IC-40 will kick in and shut the unit down. It's still has power, which is fine, but it wont make chlorine. The IC-40 itself plugs into a port on the bottom of the ET box. This gives the unit power, and lets the ET box control and "talk" to the IC-40.
For a single speed, 240 pump, the breaker is wired into the pump relay as above (each hot goes into each of the 2 "line in" terminals). The 3 wire from the pump then goes in to the "load" side of the relay. One hot from the pump into "load 1" the other hot from the pump into "load 2" and ground into the ground bus. For a 120 volt pump, only one "line" side and one "load" side get used, ground to ground bus, white neutral to neutral bus (for anybody reading this with 120 volt pump).
If you have a 2 speed or variable speed, the ET box needs a relay to take care of this.
I need more info on the pump. Is it single speed, variable speed, 2 speed? Do you have the multispeed relay in the box?
Ok, thats enough for now. Read this and post back. :-D