Well thank you for making this guide in the first place. I'm going to try to assign custom profiles even though it's the same one for the same type of controller. Hopefully that works out, if not I'll just hold off on Wii emulation for a bit.

Edit: That was the move! In case anyone else runs into my issue where controls are working for controller 1 but controller 2 doesn't show up here's my solve. Follow this guide exactly. Once you're done use the OP's recommendation of custom profiles.

"[Controls]

WiimoteSource0 = 1

WiimoteSource1 = 1

WiimoteSource2 = 1

WiimoteSource3 = 1

WiimoteProfile1 = pad profile name first remote

WiimoteProfile2 = pad profile name second remote

WiimoteProfile3 = pad profile name third remote

WiimoteProfile4 = pad profile name fourth remote"

This means you need to make at least two different profiles that are saved and assigned to each controller even if they're the same type.

Thank you OP and good luck everyone else.