I enjoy snacking on popcorn, and i recently found out you can pop it without losing flavour in the microwave.  I have always seasoned my popcorn after popping, but i am not really sure what is best with the microwave. Would it be to salt and pepper my snack before, after, or both? 
I like to season immediately after I take it out of the microwave. At that point, there is a still a little bit of steam/moisture (admittedly, not much) in with the popped kernels, and that moisture helps whatever seasoning powder you use adhere to the kernel.  Also, if you aren't doing so already, consider using a salt specific for popcorn, a.k.a. "popcorn salt." It has a finer grind than table salt and that helps it stick the kernels better. Google it, there are many brands. I use one with cheese flavor in it.  This Q also has some pointers How do I get seasoning to stick to home-popped popcorn? 