When in doubt, copy the entire contents of the source CD to the appropriate sub-folder in AmiPUP!
In that YouTube video, I was using Amiga Forever, so I copied the "disk.info" file and the "Amiga Files" folder from the AF CD to the "Amiga Forever" sub-folder, which is enough to complete the installation. You will also need to copy a 3.1 rom file (renamed to kick.rom) to the other folder on the AmiPUP desktop.
Don't forget to create a save file the first time you shut down, or you'll need to do it all over again the next time you boot!
Hope this answers your question.