There is no right or wrong hole as there is no polarity requirement by the pump.
JPT - junior power timer connectors. Easy enough to remove - fine screwdriver down the square holes each side of the connector and twist so that the flat is at 90 degrees to the tang, remove screwdriver, ( one at a time will do it) to depress the tangs, then just pull out. Just lift the tangs back up to re-use.