His guide is fine I don't see any problems with it. The directory thing you are talking about is quite simple. This would be where all the patches can be obtained from. Example all ACME patches are found within

then by adding the name for each patch it will give a link when autopatcher requests it.
But really you could ultimately make each patch a single directory yourself if he doesn't have much of a restriction on it.
Example would be
Patches Directory = www.
Bundle patches:
5000 = acmeeo.com/patches/fivethousand/5000
etc
I didn't write the program but I guess it's possible if you wish to store them in more then 1 location.