Naw you still fill them all the way.
Can I suggest pricing out tray/res combos at the hydro shop? Rubbermaid tubs need to be reinforced with a wood exoskeleton to hold all that water... my buddy lost the security deposit on his cottage when his reservoir (40 gallon rubbermaid) collapsed under the weight of the water... The white Botanicare plastic is CHEAP and designed to be used as a system, and you can use the res to put the tray on. 4x9 is HUGE. Try 4x6 tops if this is your first time out, and you will want to run at LEAST a 600hps on a mover over that space, up to 2 hps1000s.
Clay pebbles in e&f get flooded 6x per day spaced 4 hours apart for 15 minutes.
Veg your clones for 2 weeks and plan to finish them in 1 gallon polypots, or veg them 1 week and finish them in 6" quart squares packed in tighter.

You REALLY want a mother plant for any hydro system other than DWC by the way. Makes your life easier- larger plants suffer root rot in e&f systems more easily than small plants.