Thanks to everyone that replied. I figured out how to solve this problem. Below I will list in steps what I did so others will not have the same issue:
1. With your Wii turned on at the channel menu screen, press and hold the red sync button on the Wii for 15-20 seconds. This will unsync all controllers. You will see the blue light on your Wiimote turn off when it has been unsynced. Remove the batteries out of any Wiimotes.
2. Turn off the Wii by holding the power button on the Wii.
3. Turn on the Wii. You will see the typical splash screen that starts when the Wii is turned on. Here there is a prompt that says something like, "Press A to continue". Just wait a few minutes and the Wii channel menu will load up without having to press A.
4. The channel menu loads, but at this time, no controllers are synched to the Wii. Now is the correct moment to sync the Wii U Pro controller so it will register as controller 1. Press the red sync button on the Wii, and then the red sync button on the Wii U Pro controller. The Wii U Pro controller will flash blue four times.
5. After syncing the Wii U Pro controller, you will now need to sync a Wiimote to navigate the channel menu. Once the Wiimote is synced, launch the Snex9x app (or any other Wii U Pro controller compatible app). The blue light on the Wiimote will indicate that the Wiimote is in the player 1 position, but disregard this.
6. As the app is launching, remove a battery from the Wiimote. This step may not be necessary, but it works for me.
7. Once the Snes9x (etc.) app is launched, touch any button on the Wii U Pro controller. After several moments, the controller will register as player 1. The blue light on the Wii U Pro controller will be on in player 1 position. You can now load up any SNES game, as the game is recognizing the Wii U Pro controller as player 1!
8. To keep the Wii U Pro controller synced into the player 1 position, power off the Wii by pressing and holding the Wii U Pro controller power button when you are finished with your game. The next time you want to turn on your Wii, press and hold the Wii U Pro power button to do so, and the Wii will activate. As the Wii has turned on, it has recognized the Wii U Pro controller as controller 1. You will have to turn on your Wiimote at this point however to navigate the channel menu. Again the blue light on the Wiimote will be in the player 1 position, but once again, disregard this.
*** An important thing to remember is that any time you load an app, such as Snes9x, etc., the app will automatically search for a controller to sync with. If you have batteries in your Wiimote upon loading the app, the app will default sync to the Wiimote as player 1, instead of the Wii U Pro controller. So, as your apps are loading, kill your Wiimote. As I mentioned above, this may not be necessary, but this method has consistently worked for me to keep the Wii U Pro controller in the player 1 position.
I've been playing Castlevania - Circle of the Moon the last few days with the Wii U Pro controller and have been loving it. It just feels a lot better than playing with the Wiimote, and it adds a Symphony of the Night controller feel to the whole experience.
Feel free to reply or message me with questions! Let me know if this helps!
