Xbee wireless programming with Elecfreaks shield

I am trying to use the program feature of the Elecfreaks shield http://www.elecfreaks.com/store/xbee-shield-with-logic-level-converter-shd08-p-175.html with the Xbee transmitter being a SainSmart XBee USB Adapter for Arduino UNO MEGA R3 Mega2560. The SainSmart already has the CTS and RTS pins wired to the Xbee so I don’t think any mods are required. Thee Electfreaks shield advertises “programming hardware”. Looking at schematic the Xbee CTS pin is connected to a transistor that pulls reset low however LadyAda shows using the RTS pin not the CTS pin. Does anyone know how to make this work? I’m using digimesh 2.4 pro Xbees for this.

BTW when the shield is installed on a Mega or Uno the board can no longer be programmed from the USB. I can’t see why this is by looking at the schematic.