The XBee module can be used connecting it to whichever UART of BBB you want or even on another board to obtain a remote, serial low level access to any resource. In this picture the XBee is connected to UART0 to supervise console output of BBB during startup.
The RF module can also be connected to the Arduino board, via the second header which uses a 5V to 3.3V level shifter.
The use of a perfboard with soldered wiring allows a very high component density.
In the pictures the components placement and the schematic diagram.