control 2 outputs with a single input and pid
Yes, you should use PID. However, you have choices as to how the PID relates to the current through each electromagnet:


Use one PID system, driving each electromagnet equally (you might even wire them in parallel or serial and only use a single driver)
Use two separate PIDs, one to drive each electromagnet


The second option would be more flexible, but a LOT harder to configure, especially when you aren't familiar with PID design. The first design would be much simpler, but wouldn't work with your "multiple repulsion" model.

Since you state that the permanent magnet is on a "pendulum", I'll presume that you don't have a counterweight, and so there will need to be a steady-state upward force to counter gravity in any steady-state position. You might consider reversing your top electromagnet so that it, too, attracts; that way "pendulum too low" would be translated into "make both electromagnets stronger", and "pendulum too high" would be translated into "make both electromagnets weaker".

I expect you will have trouble with the nonlinearity as the permanent magnet approaches each of the electromagnets. If possible, you might consider adjusting the shape of the permanent magnet (perhaps with pole pieces) to moderate the change in force as it approaches each electromagnet.