Do they work together? If both have to run MW from there own menu which should I start the game from? silgrad is killing my FPS.

Set FPS Optimizer to launch MWSE, or better yet MGE which includes MWSE and they play nicely together.

^ how do I do that?

Sorry, it's MWE that launches FPSO & MW. Just load run FPSO then run MWSE without stopping FPSO.