I have installed Homebrew through the bootmii without issues, BUT when I try to use any app my Wiimote will not function in any of the apps. It is fine while playing any of my games, it's just in Homebrew. I would like to experience the awesomeness I have read about, but right now I can't without any wiimote functionality. Thanks.
It would be nice if you said which app. If you have an unofficial wiimote, most homebrews (if not all) will have issues. Moreover, if it's a 'recent' official wiimote, a lot of homebrews won't support it either, since they were created before it exists.