The BootMii folder goes in the root of the SD card, not the apps folder.
cIOS14 isn't related to the Shop Channel at all. And yes, it does mess with SSBB and the Metroid Prime Triology. Those two games are Double Layered disks. cIOS14 doesn't read the second layer correctly. You can't play...
--Download WiiSCU (Download the newest version, 0.23).
--Open up the .zip file.
--Open up the apps folder.
--Copy the folder in there (Wii System Channel Updater it'll probably be called) to the apps folder on your SD card (The path should be something like *:\apps\Wii System
Channel Updater...