Howdy Tazard, I would recommend running (at a low flow) the water from the start thru to the end. This will 'train' the roots to grow into the reservoir, nature causes the roots to seek out the water flow naturally. This is one problem with bottom feed DWC, I have had roots grow into the irrigation lines clogging them up. Keep the water temperatures down (65°-70°F) and good luck with Your grow.