ppf-o-matic is handed a BIN file produced by CloneCD. It is also handed a patch to apply to that BIN file.. The source for the patch will state which version of the games can take that patch (it's a location and checksum thing).

The patch(PPF) is encoded with original information (esp. the CRC) so when you run ppf-o-matuc, it checks that the BIN file is the one intended for this patch. The patch is then written into the BIN file which can then be burned to CD-R.

If the PPF doesn't match the BIN, then don't bother - the game won't work.