Just run your CO2 when the lights are on. I would suggest shutting it off 30 minutes or so before the lights go out.
The bubble counter is nice because it lets you see how much you are increasing, or decreasing when you adjust your CO2, but it doesn't really tell you much about how much CO2 is going into the tank or what the CO2 level is. Every tank is different, and how you are dissolving it into the water plays a huge role.
2 bubbles a second is probably plenty safe on a tank that size, so start there and slowly increase every day or two for the next couple of weeks until you are confident that you have enough CO2 in the water. A bubble counter can be helpful to give you the confidence to increase.
Depending on your lighting, you may need more or less CO2 for optimal growth. Just be careful and adjust slowly since this is your first time setting up an injection system. It's better to spend the next 2 months dialing it in than to suffocate all of your fauna.