Yup, that's what I do with mine. I also leave my A123 batteries in the plane for charging. I use dual switches even on my little 50cc bird with a single 2300mah A123 having dual outputs. One output goes to a HD switch with a charge port and then to the Batt/Bind port. The other output goes to another HD switch and then to the Batt/Data port. I charge the models with dual rx batteries, one battery at a time. I normally hook up the charger (If it's the CellPro 10) to the ignition battery and to one rx battery. Then charge the remaining rx battery.

On the models with the big PowerSafe rx's, those have "Fail on" softswitches and those will draw some power while turned off so I disconnect the batteries after a days flying on those models and then you can charge both rx batteries at the same time.