Put the game disk in your Wii. Start Gecko OS. Choose “Launch Game.” At a certain point, GeckoOS will tell you it is looking for cheat codes for the disk’s game id. If it doesn’t find any, then you’ve done something wrong. In that case, check your SD’s /codes/ folder in WiiXplorer or with your PC and make sure you have a GCT file there with the appropriate game id (Gecko will briefly display the game’s id code before loading the game. You can also find out your game’s game code here).
If GeckoOS does find the appropriate GCT file then it will load it automatically and you will be able to cheat to your heart’s content. If you want to stop cheating, exit the game, then either run it directly through the main Wii menu, turn off SD cheats in the GeckoOS config options, delete the cheat file from the SD:/codes/ folder, or simply reedit the GCT file in the way you created it, but unselect all cheats and then overwrite the existing file.