It is within each port's own 'Configure' button.
They will be handled entirely in the GameCube Controller Configuration window. The controller order on the PC does not have to equal to GameCube controller port order. The emulated GameCube controllers themselves are referred to as 'Standard Controller' in the dropdown menu. In the Gamecube Controllers config area, you can configure or disable the emulated GameCube controller ports. The main controller configuration window will appear, as seen in the screenshot below. To open and manage the controller settings for Dolphin, from the Dolphin's main window, navigate to Options -> Controller Settings, or simply click the 'Controllers' button.
