Do you know how to get ps3 controllers working in general? I can't figure it out.
In general? Yes. I'll go ahead an expand that to controllers as a whole.
1) It must be a USB controller, or one you can patch through a USB converter. If it doesn't plug in through a USB port, it will not work.
2) You gotta install the drivers. That's what lets the computer recognize that you're using a controller to begin with. If it doesn't happen automatically when you plug it in for the first time, a quick google for "----- controller drivers for [your operating system]" will find you both the drivers and how to install them properly.
3) Find the input settings. On pretty much every emulator, it's either under "Input" or "Configuration". Here's what you're looking for on SNES9x, Dolphin, and DeSmuMe.
4) Make sure your controller is connected, because you're about to set your inputs. You should get a screen something like this. Click a box, make your input on the controller. Don't hit enter, don't hit arrow keys, don't type words, and don't click the mouse. Use the exact input you want to be mapped to that spot.
Notice that I have two configurations, labeled "Joypad #1" and "Joypad #2". This corresponds to the controller port used in the game (although some emulators have a fifth one, that I still haven't figured out). My Xbox settings are currently the P2 settings, so I can't use this one for single-player games unless I swap it over.
Additionally, some emulators, like Dolphin, allow you to save controller profiles for quickly switching between keyboards, controllers, and other player preferences.
Also, I don't recommend using analog sticks for traditionally D-pad inputs. Sometimes, depending on the sensitivity of the stick (which can be adjusted, btw), you may get continuous inputs or move over two spaces when you wanted to go one.
Fun fact: if you want to use these same controllers for Steam games, you're in luck! You only have to set up the drivers, you don't need to go configuration hunting.