I did the same thing but with a little differences.I drilled a hole below the motor so the co2 will be chopped into smaller pieces like you say,it is very effective...so far still nothing wrong with my filter.
80 g, Eheim Pro II w Hagen Surface Skimmer, TetraTec IN-1000, JBL Aquabasis and Sand subtrate,
1st 40w Lighting: 40W Marine Glo
2nd 80w Lighting: 2 40W Power Glo
3rd 80w Lighting: 2 40W Aqua Glo
Whole set of Azoo fertilizers
3.8 kg Pressurized co2 tank