I actually just put in my DIY CO2 about a week ago and I followed the directions pretty much from
here.
I've heard that that second bottle does help collect impurities cause how clean can you really get a 2L bottle of Coke?
Plants use it during photosynthesis. The fish in the tank give off CO2 as by product of respiration, but not enough for the plants to thrive. Adding CO2 by this method makes the plants that much more happy.