While in your wii home, press the sync button on the controller, then press sync on the console. The lights will stop flashing. While in your wii loader (assumed it supports it, usb loader gx does) or nintendont, press a button and it will connect immediately. If it connects as 2P, unplug your gamecube controller or unsync your other controller (likely, a wiimote) by long-pressing power on the controller.
If your wii U pro controller is not official, you may get problems. It may even not work at all, even if is working fine on wii U.