For whatever reason, many options in the emulator are unavailable to me (they are simply gray so I can't click on them to change them) and I don't know why. Don't sue me, I just installed Dolphin?
Which options specifically are greyed out? If you can name them or take a screenshot, it might help to diagnose what's going on.
Usually this is because a game is currently running. But like Shonumi says, we would need an example of one of the grey options to know for sure.