Depends on what the controller is expecting. If it doesn't have a way to set the number of magnets, then the more magnets, the faster it thinks the pedals are spinning (the more pulses per revolution).
If it does have a way to set the number of magnets, then when set correctly to what you've got, the higher the resolution (smoother PAS) it can have, depending on how the controller is designed/setup.
There are magnet discs with as high as 24 magnets availalbe that I've seen, and as low as 5.
If the controller does not have a PAS connector and/or any PAS stuff in it's setup/LCD, it may not be capable of it. WIth no info on the controller, you can only guess and experiment.