The OF will be on your memory card and will not be edited at all (unless you choose to do so using PESFan Editor - though this will be done on your PC and you will then need to re-input onto your memory card).
With patches you will be patching the e_text and o_text mostly (if using English language) and sometimes s_text - the e_sound, o_sound and s_sound files may also be edited for chants, music etc. These files are within the .iso file you will need to rip from the original copy of your game (using ImgBurn) and you will not be touching the OF on the memory card.
Once you've patched the x_text and/or x_sound files, you will need to rebuild the .iso file, ideally using CD/DVD Generator 1.5 and then burn the .iso onto a new DVD. To play this new DVD you will need a modded PS2 or SwapMagic 3.6+.