Once you've formatted your HDD to FAT32, MBR Boot Sector, put one Gamecube ISO and one Wii WBFS in their proper structured routes:
Gamecube Games: HDD/games/Folder with name of game/game.iso.
Wii Games: HDD/wbfs/Folder with name of game and [ID OF GAME]/ID OF GAME.wbfs
Launch Nintendont, and upon loading, choose USB. It should load your Gamecube game(s) right away.
Launch USB Loader GX, and even if it doesn't load the WBFS games right away, remember to choose "Settings" and then tell USB Loader GX to use USB instead of SD (if you had SD choosen previously) and it should read both your Gamecube and Wii games.
Regarding emulators, such as RetroArch, Snes9xGX, FCEUGX, VBAGX and others, remember to tell them to load from USB and provide routes when needed.
Again: If you're still experiencing problems with your HDD, opt for using another brand.
And if you're encountering other issues, post them and we'll try to help as soon as we can, and in my case, as long as I know how to solve the issue, I'll provide help.