It needs to be on all the time the lights are on, you don't have to run it during the dark period, but I do. I like my girls to have plenty of fresh air.

Do you have an intake and outtake for the air? This is not so important now, but as the plants get larger you will need fresh air coming in and stale air coming out of your grow box, as well as circulating the plants.

If you do add an intake and outtake, make sure the intake is low and the outake high. Computer fans are good for this, I use a 3.5" computer fan as an outtake and just have a hole as a passive intake. You can use black stockings to stop light leaks through the intake and outtake.

Also I would try to find out what spectrums the bulbs you are using are and take Covert Carpenters advice.