Ignore the patch file, take the .dols rename them to boot.dol and put them in their proper folders in the app folder. In the Wii or vWii system menu (the channel select menu) hit the red sync button on both your Wii/WiiU and on the Wii U Pro controller, the controller LEDs will blink and then seemingly not sync, and the LEDs will go out (but it actually has synced), now go to the either emulator and hit any button on the controller as soon as you're in the emulator (you can do it as soon as you get to the game select screen), and the controller will be synced. Let me know if that doesn't work for you.
Thank you so much. It works perfectly now!
I just figured that I already had it synced with Devolution, so it should be synced up with the rest of the Wii. But! Apparently not?
I synced up all 3 of my Wii-U Pro controllers on the Wii home screen, then they instantly worked in the dols! I even turned them all on, and they all came on accordingly and each one's blue LED lit up accordingly to it's Player number. I'm very happy with this.
Even better, the controllers still work in Devolution without re-syncing back to Devolution's methods. Very awesome.