Thanks for the help everyone. I finally got everything working and am just about finished loading up the last of my games. Have almost the full library of everything I want for N64, Gamecube, Wii and Wii U.
I was approaching all of this from my previous experience with ROMs, just being able to download from ROM sites and load them up in an emulator.
Obviously this is a different process and using the ROMs I was finding didn't work. Once I installed windows on my Mac and installed Wii U USBHelper and TeconMoon VCWii injector everything went pretty smoothly from there.
I now have all the games I want to play on my Wii U homescreen as launchable titles and can even play the Gamecube games in Nintendont with the Gamepad, without having to load up the VCWii first and then load Nintendont, just boot straight to the game.
Being able to use the gamepad is nice, though if there were a way to use TeconMoon to boot a Gamecube game from the Wii U homescreen but use the Wii U Pro controller instead of the gamepad, that would be amazing.