One reason that the schematic is so confusing may be just that it's so simple. The only real connections between the XBee module and the Arduino board are RX, TX, +5V, and GND. You can still use the +5V / GND pins on the Arduino - if you can get to them under the shield. Also, note that the transistors that connects the module to the reset line of the Arduino isn't mounted on the shields, because in its default configuration, the module would keep the board reset continually.
The contact points next to the XBee MaxStream module are there for advanced users who know what they are and want to use them. If you just want to use the module to send data to/from the Arduino, you don't need them. While it's possible to connect sensors and actuators directly to the XBee module, you probably wouldn't need to do that with the shield (just connect the sensors and actuators to the Arduino).
Are you looking to send data from an Arduino w/ XBee shield to another XBee (on its own, without an Arduino)? Or between two XBee shields on Arduino boards?