Should I wait until my lights are on to make these changes?
And should I turn the co2 off at night, even when levels are indicated low?
Are you using DIY CO2 or pressurized CO2?
In the latter case, you can turn off the CO2 at night as plants do not consume carbon dioxide when they are not performing photosynthesis.
As for when to make the adjustments, you can do it any time, really.