Bootmii

I've just installed BootMii via, Bannerbomb and I am a bit confused. After I installed BootMii I exited HackMii Installer and it went straight to the Homebrew Channel then just as I clicked "Return to system menu" I saw "Launch BootMii" I clicked back on the Homebrew Channel and started it and a message appeared saying something about the system files are corrupted. Is this meant to happen, and have my files been backed up?

reply asap thanks bye !

As soon as you started BootMii it gave that message? Or did you return to System Menu/boot System Menu from BootMii? Have you installed/run anything else homebrew wise? e.g. preloader or a WAD installer?