Okay, what should I do if I use the Homebrew set?
Well, if you downloaded the full WiFi set for homebrew rather than just the .gct you could just replace everything and not have to worry about looking for where the folder is specifically.
If you want to be super tech savvy though...
You'd download the WiFi safe homebrew set (not the GCT) and you would go to private/wii/app/rsbe/pf
and in pf you should see a folder called, "system". You'd drag and drop that into the same location that's on your SD Card.
You'll have to replace that same folder and the gct every time you switch between offline and WiFi. So it'd be a good idea to have a copy of each. Or just replace the files wholesale as I said above.