The GamePad can be used without any prior set up, but all other controllers require changing settings inside the Unity Editor before you can use them in your game.
Setting up Additional Controllers
Go to Edit > Project Settings > Player from the main menu.
Click on the ‘U’ logo for the Wii U in the Inspector.
In Other Settings, scroll down to Enabled Wii Controllers.
For Wii Remote Count, enter the number of controllers in addition to the GamePad that you want to all to connect to the Wii U (acceptable values are 0-4). Wii Remote accessories do not count. The Pro Controller and the Balance Board each count as one remote.
Check the box for each type of accessory you would like to use.
Info
You can sync controllers to your devkit either in game or anytime while the System Config Tool is running.
If you mark in the Unity editor that your game supports a controller, you must also make note of that in your submission documents when submitting your game to Lotcheck.