When using a diffuser, The only thing that matters is that the CO2 is dissolved in the H2O. The best way to accomplish this is to allow the bubble maximum time in contact with the water. That being said, agitation helps the process, so letting it run through the filter is probably going to net you slightly better results as the bubble is forced to endure maximum agitation. HOWEVER if your filter outlet agitates the surface, its a moot point since gas exchange will happen at the point of surface agitation. I place my at the lowest possible point in my tank on the end where the outlet is. Thes allows the "blown across the tank" effect which gives me consistent results.