Carbon filters work by trapping airborne particles in the pores of the activated carbon inside the carbon filter. You need to draw air through the outside of the filter (passes through the carbon) and then out through the internal exahust of the filter itself. If you can vent outside, do so, as it creates negative pressure in the room which can be used to pull in fresh air from elsewhere. You have to make sure your fan has enough power to draw correctly without too much of a static load as well. Open to debate I suppose(for some) but most would agree it's best to pull clean air out of a carbon filter, than push dirty air through it. Why? Because air that hits the fan blades that has been 'scrubbed' already has less particulants to stick to the fans blades, possibly slowing it down or throwing it off balance. If you PUSH the air through, the air is still 'dirty' and likely to contain a higher amount of particulants. Common sense, really.
Good luck!