Technically you only need one switch with the breakout box or you could directly wire one in... instructions for how to do that are in the manual. I use two just in case one of them fails for some reason. Mine will run the ATO pump at any time. Whenever it does come on it runs for at least 30 seconds because I didn't want the pump to constantly switch on and off ever second in response to surface agitation in the sump.
Just keep reading and working away at it. I know the system is confusing as hell at first. Did you buy your unit new or was it used? I was just thinking that if it was used you should consider reseting everything back to the factory defaults so that you have a clean slate to work with.
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