Additional parameters
Reboot
For rebooting ArduPilot go to the Vehicle Setups
menu and there choose
Parameters
tab. Further click on Tools
and Reboot Vehicle
after.

Telemetry
For UART radio connection use SER2-ADC (ttyAMA0). To change port configuration you can use SERIAL1_ parameters.
Since v1.3 connected USB radio (ttyUSB.Radio) will be recognized. To change port configuration you can use SERIAL2_ parameters.
Both ports have default baud rate 57600.
GPS and Magnetometer
For external GPS (UART) and Magnetometer (I2C) you can use SER1-I2C (ttyS0) port. To enable GPS in ArduPilot you also need to set GPS2_TYPE parameter to AUTO and reboot.