You can also assign the Wii Remote to connect it as an emulated controller by selecting 'Connect Wii Remotes for Emulated Controllers'.
In the Wii Controllers config area, you have the option to use real or emulated Wii Remotes, as well as choosing to passthrough a Bluetooth Adapter (see Bluetooth Passthrough) or emulating the Wii's adapter. 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.