I had this same problem. I have a 20g, the bottle was about 2.5 ft under the tank, and the bubbles would not reach the water. I hooked up a second bottle connected to a "T" and the combined pressure would push bubbles to the water, but a fine bubble air stone provided too much "back pressure" The only thing I could do was leave an open ended tube in the water, and every 20-30 seconds, I'd get a burst of 10-20 bubbles over a 2-3 second period.
From experience it seems unless the bottle is right beside the tank, it won't work.
I tried the paintball co2 from the thread on the diy page and it works great.