If I understand your description correctly you have the 50A GFI installed in the main panel which is feeding the 20A and 30A in the subpanel. If so the subpanel and spa are GFI protected. I personally would have done the same thing and don't see why three GFIs were recommended.
I'm not sure what you meant by "configured the neutral lead in the main box". The correct thing to do would be that the white pigtail lead which is permanently attached to the 50A GFI should be connected to the neutral bar in the main panel (where all of the other white wires are connected). Then connect the white wire leading to your sub-panel to the "white" or "neut" terminal on the GFI. Do not connect the sub-panel white wire directly to the main panel's neutral bar.
Out at the sub-panel all white wires should be connected to the sub-panel neutral bar. Make sure that the neutral bar is not bonded to earth ground. The sub-panel neutral bar might have come with a screw or jumper which could be used to connect it to the metal enclosure of the sub-panel itself. You don't want to do that in your situation. All neutrals need to stay isolated from a ground connection after exiting the 50A GFI back at the main panel.
Also out at the main panel the green or bare earth ground wires need to be connected to the sub-panel ground bar. They should not be connected to the neutral bar. (Even though you might have seen grounds and neutrals connected to the same bar back at the main panel, it's not OK to do it out at the sub panel).
At this point, turn of the 20A and 30A breakers and turn on the 50A GFI and it should not trip. If it does either the GFI is bad, you have a neutral and ground connected somewhere, or you damaged the insulation on the wire.
Next turn on the breaker (20A?) that runs the pumps. See if you can run them for a while without tripping the GFI. After that try turning on the other breaker and raise the setpoint to run the heater. If either of these steps fail you'll know where to look for th eissue.