you know i been using my trays for years with in and out in the same side but lots of people been setting them up with duel lately??
for a true ebb and flow i dont think it matters much but when converting to an swc/dwc i think it matters alot since the root mass will restrict water flow and create dead spots the multiple in/outs really makes a big differnce..
You have to play around with the swc a little, for awhile you will still ebb and flow until you have good root mass, but you will do it very frequenty (unlike ebb and flow), you will cycle the water every half hour or so and once at night, when you get alot of root mass you will put the riser in and only cycle the water out every few hours by turning the pumps on, at that point put your airstones on full time...
Am I making sense?
When no water is in the tray - stones off
eventually you will always have water in the tray - stones on all the time, but the pump will cycle the water from your res every few hours from both ends.. you can easily just put a T in your pum line and add an over flow...