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. If you need help, or want game-specific configurations, see the forums.
This page explains how to configure controllers in Dolphin, assuming the controller is connected and working with your system.
