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I don't think there is a "proper way" I think most guys who did this just used a 1 inch bit and drilled....I suppose you could use a quarter or something and map out a pattern
I am sitting here staring at my air box. and I guess I was confused for a second thinking that I was supposed to put the holes behind the air filter. I just realized that if I do that there is no way the air would ever be filtered.