@ruthless4u For an end user, it's just a matter of fiddling around with the app and figuring out what features and settings get you the gaming experience that you're looking for.
Fire up a game in nestopia and compare it to fceumm. Try a different color pallet. Compare the audio. Change your settings and see how it affects your game. Once you get a hang of things, you can read up on what each feature does and why they exist, like threaded video, audio filters, etc. Why should you use one emulator over the other? Why should you care about performance versus accuracy? And even if something goes wrong, nothing is permanently broken; just start from scratch, look it up online, and figure out what works and what doesn't.