what do you mean by "i have homebrew installed" ? is the hbc still present? use the option of the guide "hbc still present" to run MMM etc and the hackmii installer to reinstall hbc to ensure hbc is running on IOS58 (chapter1).
so if you updated but the hbc is still present, the update killed your cIOS and you have to re-softmod (chapter 2)
when done with the guide you will be able to play games off an usb harddrive (like getting apps in chapter 3).