You want your CO2 to run when the lights are on. That is when the plants can use it. Most people start it say, 1hr before lights on then turn it off 1hr before the lights. You want to shoot for 30ppm of CO2 in the aquarium. You can look into drop checkers or a ph meter to help with this. Read more into the sticky's here and another great resource is Barrreport.com