When there is water in the skimmer, it would work normally. If the water dropped below the skimmer opening, the pump would suck the skimmer dry and then draw air (bad!). But if you have an equalizer port for the skimmer, there would be some sort of flap in the skimmer that would drop into place once the skimmer ran out of water, so that the pump would then draw water from the equalizer port instead of air from the skimmer. I've never seen one myself, but I think that's what you're describing.
The other two suction ports, by the light, should go to the same thing (probably your water feature), as suction lines are supposed to be in split between two openings, just like what yours looks like (the two work together to prevent entrapment under water).
If looks like you have two feature pumps, so it's possible that there is just one port for each pump, which is not ideal, safety-wise. Then another pump for the spa (that pump's suction port would be in the spa). And then the booster pump for the vac. The booster pump should draw its water from one of the return pipes on the pad, not the pool. It's "boosting" the pressure from your main pump. Looks like they connected it underground, which is a little unusual.
Does the pump nearest the left wall have a label?
That's a lotta pumps!