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Drill the wrong side of the box and the air you'r engine sucks in will bypas the filter. i.e. your engine will be eating stones, dust, small dogs and old ladies. Make sure that you drill the side of the box that take the air through the filter.
Here Stateside we're keen on putting in cold air intakes, be they K&N or whatever... but in the case of a turbo'd car, it's necessary to not draw in preheated engine compartment air, so a common mod is to drill a hole through the bulkhead into the fenderwell and mount the cone filter down there. This also eliminates a lot of restriction common to the stock setups.