An option file is a file that can be saved onto a Memory Card that controls things like player names, in-game edited kits, transfers etc etc.
A patch is a collection of files that are inserted into the games inner structure. These files physically replace some of the graphical files present in the game. This can only be done by using your PC. Patches change the graphical 'look' of the game, i.e real sponsored kits, new balls, new stadiums and even new chants and faces. All this info is stored in the game image and is therefore unaffected by the option file.
The threads in bold text at the top of the Editing section should help you. Once you've played patched WE/PES there ain't no going back!