A flashlight is a handy device for this. Shine it through the caliper while you look through from the other side. There should be a minor but constant clearance as the wheel spins(do it slowly). When you tighten your skewers, have the bike upside down and lean straght down on the wheel to place pressure on the axle to keep it seated in the dropouts. Sometimes the action of pushing the QR can drift the axle over. If there is no clearance when you do this, then readjust your caliper so that you have equal clearance on both sides. Then the wheel and caliper are set to a reproducible standard.