sorry for a simple and vague question, but I don't know much about hardware since I've focused on software where we don't have the constraints of actual physcial reality.

I'm beginning a project that requires me to run a (hopefully) large number of electromagnets using output from the computer, this would hopefully be in the range of 50-60 magnets. These are being run by an FFT which for now I want to run off my computer.

Is there some easy technique to encode several values into one signal, such as using PWM and using the width to determine an output to go to, (such as from the arduino board into another board to "split" the signal, 1-10% width goes to output 1, 10-20% width goes to output 2, etc) or am I better off using / designing a system with more outputs (or just using more boards)

I suppose ideally I could run an FFT off a DSP chip but since I'm new to using hardware I think it would be quite a task to translate the FFT into 50-60 outputs.

Once again, sorry for a basic question and I hope that someone has suggestions for a place to start looking (I don't plan on building for a few months so I have time to research beforehand).

Look at the posts where folks are driving many LEDs - the concept is the same, but you'll be driving bigger loads if your magnets are very large.