First time with CO2

I have not had good luck with Live Plants in the past, and assumed 
that it was always due to poor CO2 content in the water.  I had them 
in a 29 gallon tank with one GRO-LUX and one Cool white ligh.  
Ammonia and Nitrites were not even trace.  I was told by the pet 
store that I frequent not to be concerned with nitrates as the plants 
would 'eat' it for food.  
Yeterday I constructed a CO2 generator out of a 20oz soda bottle, 
some airline tubing, and a small bottle.  I am using yeast and sugar 
to generate the CO2.  I moved all of my plants to a small desktop 
aquarium (5 gallons) and added the CO2 rig to it.  
My concern is to water quality.  Should I stop doing water changes to 
the tank?  Should I add the Flora Pride?  Will my Ammonia, Nitrates, 
Nitrites, PH, etx. be affected by the CO2?