What I did, was buy a K&N drop in replacement filter, and then swisscheese the airbox with a large drill bit (but not around where the crankcase vapour from the emssions thingy gets re-sucked in by the filter).
I don't recommend this - as with all pod filters without any thermal sheilding , all you're doing is sucking in hot air. I ended up taping all the swiss-cheese holes up, and going back to near-stock. Never got around to sorting the cold air intake out properly.
Best bet... if you're alreaady bought the pod filter.... would probably be house it within the stock air box, and then have some cold air intakes feeding up to the front of the box (and cut holes in it to suit). See pics of Nark's car for pics of the piping & sheilding.
BTW the "other box" you talk of, underneath the air filter box, is the 'stones/dirt catching thingy'. Most people remove it. I took mine off & lost it.