I went back and looked:
The gameini's are in your main Dolphin folder > Sys > Gamesettings. Most game's IDs are already listed in the folder, I did, however have to make a new ini file for a couple of my games. To find the gameID you go to the Dolphin GUI, select the game, right click, click on properties, then go to the "info" tab in the Properties box that comes up.
One thing to keep in mind, since this is in your main Dolphin folder, if you update your Dolphin install make sure to copy the gamesettings folder first so you don't have to do all of this over again (the controller profiles are saved in your Documents folder, at least for me, so they should be safe, just need to copy the gameini's). In fact, I have a copy of the "Gamesettings" folder saved somewhere else, just in case.