Within Wii U USB Helper you click a button to prepare your SD card for use with Nintendont, selct the game you wish to play, then browse to the gamecube iso file,
which you have already downloaded, when prompted and it does the conversion to the format required for launching as a channel with WUP Installer.
Custom Firmware is required (cfw) and you need to use the correct region for your WiiU.
I have my gamecube games stored on sd card for use within Nintendont and I simply browse to the game I wish converted to a channel.
Working great here, but it is limited to the games that have been included. More are being added regularly.
Currently includes:-
Animal Crossing
Baten Kaitos Eternal Wings and the Lost Ocean
Billy Hatcher and the Giant Egg
Eternal Darkness: Sanity's Requiem
F-Zero GX
Kirby Air Ride
Luigi's Mansion
Mario Kart: Double Dash
Paper Mario: The Thousand Year Door
Pokemon XD: Gale of Darkness
Skies of Arcadia Legends
Soul Calibur II
Star Fox Adventures
Super Mario Sunshine
Super Smash Bros. Melee
Pikmin and The Legend of Zelda: Four Swords Adventures were added today, but I haven' tried those yet or Baten Kaitos, which I think is the first 2 disc game to be included. It prompted for both discs and completed the conversion process so I am optimistic.
I will be surprised if Four Sword Adventures works, as I thought Nintendont didn't have GBA support, but I've been surprised before.