You want the gas swirling around inside whatever chamber/reactor/filter you connect the CO2-hose to as long as possible.
If you connect the CO2 to the outflow of the chamber/reactor/filter you will bypass the reactor and nothing is gained. You want the CO2 to be forced through the reactor making the gas swirl around as much as possible.
So we can't say "top" or "bottom" unless we know how the water will flow in your chamber/reactor/filter.
I have the water flowing in the reactor from the top to bottom, and the CO2 going in near the bottom. So I am most likely pushing co2 right out of the reactor before it has a chance to do any good. If I am understanding what your are saying I should add the co2 at the top where the inflow of the water is. Correct?