Okay, the megger is just a very sensitive OHM meter that puts a heck of a lot of voltage on the wires. You'd just hook the megger to each of the hot wires (one at a time) and then to the ground. If you got a continuity reading with the megger between either hot wire and ground, then there's a low level short. DON'T connect the megger between both hot wires when the pump is still connected. This can and will fry the load (the pump, in this case). I use the megger all the time to prove out faulty underground UF cables that are intermittantly tripping GFCI's or breakers. How many times have you done a service call for a post light that occasionally trips breakers? Frustrating, isn't it? You just disconnect both ends of the UF, and then megger check between all the wires. If you get less than 100 meg on any pair combination, you just found a bad cable. If you forget to unhook the light end, the light bulb will read like a dead short, and you stand a chance of blowing up the photocell if there is one.
I see that your unit has three test voltages. You normally test at twice operating voltage, but I normally check everything in residential at 500 volts. Any reading over 100 megaohms is a good cable, and anything less is unusable. You can check motor windings too by checking between each motor lead and the ground terminal or casing.
"Nothing is foolproof to a sufficiently talented fool"