It depends on the furnace. usually air is go from down to up. But some furnace go other way.
One way to check, is air should go to the heat exchanger (where the fire is.) The vent level the exchanger is heating vent. Another vent goes back the furnace is the return vent where air come from. The filter is between return vent and heat exchanger. You filter should have two side. One side is all paper. All paper side should face incoming air.