I'm a bit confused by your question. Could you be a bit more specific?
Anyway maybe this part of the 1.06 readme will help.
6.) Use PPF patches
Some games need a special patch to work at all (most times
because of a game copy protection). If you have a PPF file for
that game, you don't have to make a patched ISO anymore,
just activate the file in the cdr plugin config window.
Attention: only use PPF files which are made for that special game.
Turn the PPF option off with all other games!
The plugin supports PPF1 and PPF2 files.
P.S. it also says that you can make a ePSXecutor config that uses a patch.
The only site I know of that has patches has some illegal stuff. I got a warning last time I mentioned the site.
However if you have a specific patch that you need I can probably find it and attach it to a post for you (Assuming that its small enough to attach).
The patches themselves are perfectly legal. Its just that there is other illegal stuff on the same site. So I can't link to it.
Like I said before if you want a certain patch, then I will try to find it for you and post it on these boards as an attachment. I already asked sx/amiga and he said its OK.
I don't think that you have to make a iso patch Athleon. I mean thats why Pete put the ppf option in the CDR plugin.
But I can't understand it though, I mean I got the protection fix patch from here to play Dino Crisis, but I still couldn't get pass that warning sign. why WHY?!