For the return side we can address more late but I suggest you need a couple of more pictures at different angles.
What I do see is that as the pipe exits the heater it go to a 3 way valve. That valve is OFF to the left side which appears to be the main pool returns but open to the right side which appears to be to the spa returns.
There is a small switch on the side of the controller. It has 3 positions. The middle position is OFF. Which ever way the switch it, move it to the opposite side and the valve handle should rotate 180 degrees to have OFF facing the spa pipe (to the right) and it will be open to the pool returns (the left side). This may stop your spa overflow into the pool but we can address that later. I am just trying to get the system in what is called POOL Mode. This means suction from the pool (skimmers and main drain) and return to the pool through the chlorinator (that cylinder with 320 written on it).
My understanding is that the jandy filter is suppose to help reduce the work for the de filter. No infloor cleaning system and the water feature has been disabled by the previous owner.
My guess is that this pipe that is to the right of the valve on exit of pump that goes through the small Jandy filter is your circulation to the water feature. That small filter just kept debris out of the water feature. I could not see the water feature in your picture of the pool. I see that the valve handle at the tee junction from the pump is OFF on the right side so all flow is going to the left - the main Hayward filter. The flow to the water feature is OFF. I also see a small blue valve at the ground level on that water feature pipe. It is open. I would leave it open. I assume they put a valve there so they could control the amount of flow going to the water feature.
I have two skimmers one near the spa and the other in the deep end. I believe the 3rd valve is for the suction cleaner (no longer using replaced with robot).
Once you adjusted the return side as noted in first paragraph above we can work on the suction side. So to identify which is which, you have 4 pipes, all with blue valves. 2 valves are fully open and 1 is partially open and the 4th (the one facing to the side) is closed. Is the one that is fully closed the cleaner?
To identify the others, close 2 of the blue valves - ensure 1 valve remains open - go see which skimmer is sucking water. If none that that is the main drain. Do this again by opening another valve and closing one - always have 1 valve open. Mark the pipes as SS (Shallow Skimmer), DS (Deep Skimmer) and MD (Main Drain).
Let me know if that works.