the input of water and co2 goes at the top. The outlet of water goes at the bottom.
This way, the Co2 is unnaturally forced into the water from the pressure from your filter/powerhead etc.
Otherwise, as you are experiencing, the c02 simply naturally rises to the top of your reactor and occasionally spits out in larger (undissolved) bits.
I had the same issue....foolish me, I flipped my reactor and now it is at 100%.