I am not familiar with the water bottle system, but a trick I learned by accident to make a pump quieter is insulation around the tank and suspending the pump in the tank not letting it touch the walls or bottom. Our nft system the only thing you could here was the water rushing and the air pump which I never could get quiet.

If the system you have is like a flood and drain system we run ours for 15 min 2 times a day.
But ours is a starting bed everything else sees constant flow.

cycle timing is a function of many factors. Can you post a picture of your system and maybe a bit about what your growing conditions are like?
I ran EnF twice a day for about 15 minutes also in the summer in 85-90 degree temeratures. Could have probably gone with less but the deer feasted on the plants way before I got around to testing different timings.