DIY CO2 bottles produce a limited amount of CO2, so it really pays off to use a good method for diffusing it into the water. Otherwise, you will usually be very short on CO2. One efficient diffusing method is as described here: DIY CO2 System - How to do it
I use 2 cups sugar, 1/2 tsp yeast, 1/2 tsp baking soda, in 2 liters of water. I dump in the yeast, the soda, then the sugar. Fill the bottle up just past where it necks down. Then I invert it with my thumb over the opening and shake it vigorously. Then, carry it over to the tank and connect it to the system. I use two 2L bottles, changing the solution in one every week. This is for a 65 gallon tank, and it gives me very noticeable improvement.