When you download the patches (which it sounds like you might want to do on the Japanese site), all you need to do is open the zip file and exact each item into the correct folder. It should be easy to figure out where everything goes. If it's a file that already exists, then you'll want to replace the old one. And yeah, the patches usually have a couple files and that's it (though I think the ones for .097g have more than a couple).
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