Yes, the Wiimmfi patcher also works with WBFS files. When it finds an ISO, it will generate a patched ISO. When it finds an WBFS file, it will generate a patched WBFS file.

I don't know patchimage and how it works. If you use Wiimms Wiimmfi-Patcher, you simply copy all games into the folder and start the "create-image.bat".

See the file README.RC that comes with patchimage for setting up the configuration. Patchimage will then scan PATCHIMAGE_WBFS_DIR for all matching game images (they must be in ID6 format file-name, eg.: RMCP01.wbfs) and offer to patch those. No need to copy anything, just place patchimage somewhere in your home-directory where you can easily access it.

Edit: I made the first post for patchimage 5.0 beta more clear, better readable and added some more info. Check: patchimage / wiimmfi.