You mess that up big lol
You don't rip or unpack the ISO in any way at all.
I will show you what you do, I thought the instructions were pretty clear aside from trying to work out which tools to get as the OP does not link directly to the download just the place to get the tool.
1. You download
Wit for Windows, and
SZS Wiimms Toolset for Windows.
2. You will need to run the installer for both and then reboot PC as they created the environment variables which you can run in a terminal window.
3. Put the contents of
SMG2-GamePadCC.zip and your Game ISO into a folder.
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4. In the address bar at the top of your folder window type CMD and press enter.
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5. In the now open terminal window type
wit x SB4E01.wbfs Galaxy2GamePad and press enter.
SMG2 is your game's filename. I suggest you don't have a file name with spaces, I renamed mine to SMG2 from SMG2 (USA).
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6. Then Run
wit dolpatch Galaxy2GamePad\sys\main.dol xml=SMG2-ExtraControllers-WiiU.xml
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7. Now choose which controller config you wish on the OP as you can see there are two layouts you may choose so run whichever layout you wish the commands are below.
RUN ONLY ONE OF THESE
wstrt patch Galaxy2GamePad\sys\main.dol --add-section SB4E01-SMAS.gct
wstrt patch Galaxy2GamePad\sys\main.dol --add-section SB4E01-Nvidia.gct
Example with SMAS.gct layout.
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8. Now last we have to pack the game back up again so you can inject it or get it onto your console however you see fit. So now were run this in the terminal
wit copy Galaxy2GamePad Galaxy2GamePad.wbfs
It will take a little bit to finish so when you see the prompt appear ready for input of commands it is done just be patient.
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Now You are Done!
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Hopefully, this assists you and others who don't quite understand what to do.