I did this years ago. Works great.
I have both the IC pipe and the intake pipe running through where the stock airbox snorkle hole was. (I've since enlarged it to allow both a 2.5" IC pipe and 3" intake pipe pass.)
Run with the lower plastic in place. It keeps water out of the filter for the most part, and your getting plenty of cool air there being forced into the front grille opening. Air likes to spill around the coolers as much as it goes through them. (Think about this, if you took a bucket of water, and poured it over your intercooler, some would run through the cooler, and some would run off and around the cooler. This is why duct work is so effective, and fan shrouds should never be removed. Those ducts and shrouds limit the amount of air that can spill off around the cooler v/s being drawn/pushed through it.)
So unless your FMIC is ducted, quite a bit of air is going to spill off the edge, and feed the intake filter behind the fog lamp. If you want more, build a duct that feeds the filter, but I'd take it from the front, and not try and scoop up air from below. (Too much rain water and other debris that way.)