I would strive for one valve for each bag either on the drain or fill side as appropriate.
I had a system that used these parts on my MasterCraft. This system used bags with three hoses (fill, drain, vent). As long as the through hull fittings are above the highest point on the bag when the boat is on plane, no valve is required on the drain/vent hoses (usually ported to the same through hull fitting).
Since the stock bags were near or below the waterline, a valve on the input line was most appropriate to prevent passive filling.
The side sacks were a different issue. The through hull fittings on my boat were just below the rub rail at the rear of the boat. This was a problem for the side sacks because the highest point of the bags was above the level of the fittings while on plane.
On these bags, a valve on the drain/vent line prevents the sack from draining while in transit. A duck bill style check valve prevents the bag from draining back through the fill pump.
I don't have a scanner, or I'd draw a picture and scan it in. I sold the boat, so here are the only photos I have.
The center two valves are on the input side of the stock system. The outside valves were installed to prevent the side sacks from draining.