When I run ppf o matic and I apply the patch to the bin file, does it copy the new patch to the bin file for you? I applyed the patch and it said SUCCESSFUL.
ANSWER: Yes. SUCCESSFUL is GOOD.

What do I do next, and which program do I use.
ANSWER: CDRWin as per the instructions at ####://www.psxcopyworld.co.uk. There's nothing to add. No further details to be given.

It seems as though my playstation 2 is reading my backup as a playstation 1 game.
ANSWER: You mean it stops at the Playstation symbol. It doesn't help that you don't know your modchip.

In all the circumstances I'd say you should use CloneCD which means upgrading to a Yamaha 2200 (I had to do this too). About 2 months ago someone reported getting some way with a CloneCD copied version.

Alternatively, have you visited the site ####://www.eapatcher.com to study this problem in greater depth?