Troynel, we're going to need a little more info to give an answer specific to your setup, but the reactor gives the CO2 a place/method to dissolve into the water. Are you using a sump or canister setup?
You can certainly plumb the return line of the reactor into the sump pickup, that's what I do. Running the CO2 supply line into the sump pickup will not result in sufficient absorption of CO2 into the water, that's what the reactor is for.
Usually the reactors have bioballs or some other media to trap the bubbles so that the water has a longer contact time with the CO2. The air gets trapped by the balls and small amounts are dissolved into the water little at a time.