When I turn the Aerator on auto, it works no problem. When I put it on Manual, it does not work. What could cause this?

Aerator is not for pump-in. Aerator is re-circ.

Should have a "fill/pump-out" mode.

As to Auto vs. Manual, not sure...

Pump out mode won’t work either

So do you hear the pump running but the selector valve is not moving or does you system have a pump for fill and pump out and a different pump to recirculate the water. I have two pumps on my system both have the three way values. Fill, recirculate, pump out. Mine is set up as a main at the helm and a second one at the bow. Both work independently. Those three way valves fail pretty often. Or shall I say stop transferring from one setting to the other. Last time mine failed it would fill and recirculate but it would not pump out. There is lots of info on the web on how each system works.

I have one button that’s auto, recirc, man. The other is auto, fill man. Neither will work on Manual. I do not hear anything functioning on manual.

I’m going to say that you will have a pump that runs on manual and a separate one for recirculate. I would look in your bilge and turn on your recirculate button. One pump will come on so you will know that one. The other one should have a removable cartridge type motor.. remove it and see if there is just a rock or something in there that has stopped it from turning. If not then the trouble shooting starts. Power, fuses, motor ect. Pretty easy to check. I never owned a Skeeter I hope you can see the pumps. Lol

My first guess is the switch..
Most two pump systems one is for recirculate the other for aerate..