Not really sure about how you'd patch a PS2 game, without hacking/modding a PS2 to then be able to read the game. In theory, most ps2's that have been modded should be able to play Japanese PS2 games
For KHFM I haven't heard of any succesful patches, but from what I can gather your not missing out on a whole lot, mainly just the Unknown fight and a couple cutscenes (which you can watch on youtube)
For KH2FM, I personally used this patch and had no problems with it
Xeeynamo's blog: Kingdom Hearts II Final Mix English/Italian translation [FINAL-Rev5]
Plenty of instructions on how to apply the patch to a rom there as well. BUT I only used it after I had already beaten the game/opened all the treasure chests, because theres been reports of it freezing occaisionally. All the cutscenes are in English, and there are ability lists available online so you don't miss a whole lot, especially if you've already played through KH2 multiple times on your own PS2
For BBSFM, I used a pre patched rom, and the megaupload link has surely been taken down by now so you'll have to search around a bit. Again though, you don't miss out on heaps, mainly a couple of non-canon Mirage Arena fights, though I will admit the secret episode was neat.