congrats on the filter, told you you'd like it
first, you more than likly wont be able to just have all the poop go into your filter regardless, best bet there is to net most of it up and invest in a decent gravel cleaner.
second, the more surface agitation you have lets you have a better oxygen transfer. but if you dont want to have the filter to agitate the water your probably fine anyways being as you were talking about getting an airstone.
the more oxygen the better

(dont go overboard and put 20 airstones in or anything)