Apocalypse wins.
To begin with, Poccy has the ability to absorb energy from any source and use it to increase his size, strength and durability. He is also able to rechannel this energy much like Bishop. Right there, Magneto's energy blasts should not be able to work against Poccy nor should Magneto be able to manipulate the iron in his blood. In order for Magneto to do the iron-in-the-blood-trick, he has to get a magnetic grip on it. In other words, he has to project the energy inside of Apocalypse who can just throw it back at him or metabolize it to grow stronger. This ability would also neutralize Magneto's force-field. Technically, all Poccy would have to do is touch the force-field and absorb it.
We have not even talked about Apocalypse's other powers yet. He can manipulate his body at the atomic level, IIRC, fly, levitate objects, enormously powerful energy blasts, regeneration, and, IIRC, didn't he enter baby Cable's mind and defeat Jean Grey in psychic combat? If so, that makes him a high end telepath as well.
The only realistic thing I can see Magneto trying to pull on Poccy in a fight is throwing metal. This is not going to be effective at all considering Poccy can transform his limbs and body into a form of armor that can deflect Magneto's metal projectiles.
Poccy has a huge advantage.