Well from one noob to another. . . . so would you say the co2 system ("canister") is high-pressure? It sounds like you must be doing alot of testing if you are manually adjusting the co2 flow. If you could find the "uptake rate" of your plants, then set the co2 at that rate it would be easier than manually adjusting.
The upside-down bottle is not very effective, it's typically more efficient to use a design that incorporates a powerhead/pump.
If you could explain your setup a little better, on the out-of-aquarium side, that would be helpful.
BTW, how are your plants growing? Any algae troubles?