What specifically are you having trouble with? If you have the keys you need it's pretty easy. Gamecube you do nothing but select GC Retail injection, choose your iso where it says game, click download images from cucholix's repo (this will give you your banner and icon) for gamecube you only need to go to Gamepad/meta options if you want to change the name of the game when it appears on the Wii U menu, you don't change any gamepad options it's automatically set to use you gamepad then go to build title and click build.
Wii is the same except of course you click wii retail injection to start. and get your images exactly the same way as gamecube, go to gamepad/meta options to change the name of the game. On that same page you have Gamepad emulation use this compatibility list to know if a Wii game can use the gamepad
http://wiki.gbatemp.net/wiki/WiiU_VC_Wii_inject_compatibility_list if not you have to use the wiimote and leave everything the same (as in leave no gamepad emulation) and just hit build. If the game does use gamepad you can change the gamepad options choose classic controller emulation or sometimes or I sometimes use horizontal wii remote emulation depending on the game. You just have to experiment.,
It probably sounds like it's hard and a lot to take in but it's really easy once you do it once you won't have any problems doing it over and over again, and if you get stuck you can always ask on here.