is it ok to stop flooding when its dark time?
 

When flooding your system is it ok to stop flooding when its dark time?

I dunno how this flooding works in the 2 liter bottle setup. When you say flood every 20 min, do you mean like if your lights go on at 5:00 am and off at 11:00 pm, and your pump goes on at 5:20 am then 5:40 then 6:10 then 6:30 and so on till the lights go off???

What kind of timer would you need?

Yes you don't need to water during dark period.
If your light comes on at 5:00 am then your pump should come on at the same time or a little before. The pump will fill the garden in a few minutes and if the timer you are using has a minimum on time of 30 minutes then it has to run that long. That is what the over flow pipe is for so the pump can run for the minimum on time without overflowing.
So at 5:30 am the pump will shut off and it will take a few minutes to drain.
Then at 6:00 am it comes on again. Off at 6:30 am, On at 7:00 am, so on until dark.
You can water with one hour between waterings when the plants are small or if it gets really hot, like on my back porch, I water continuously.