Wiimotes working in tandem with the emulator is not currently supported and isn't in the dev pipeline AFAIK. BBLoader is designed primarily for portables and the number of multiplayer capable units built is very low, so assuming it's even possible to do, it's unlikely to be done anytime soon while other more important functions are being worked on. If you want wiimote multiplayer atm, you'll have to disable GC2Wiimote and use only wiimotes.
The Homebrew Channel being upside down is normal, TeamTwiizers made it do that to discourage unneccessary IOS modification, which we use for the noWIFI patch and BT emulation. It doesn't affect the HBC's functionality, so it's not really wise to change it when so many other homebrew apps (like BBLoader) have their own built in homebrew menu that you can use. As for your unintended method of uninstallation, this is beyond my knowledge to provide support, but you really should have asked BEFORE manually replacing IOS modules. The BBLoader FAQ had the information you wanted.
Also stop double posting pls, use the edit button.