But of course! You can send any valid command-line-interface to JeVois from your Arduino, including a setmapping command. Have a look at the Arduino example for a pan/tilt head here: http://jevois.org/doc/ArduinoTutorial.html
Notice how we send commands from the Arduino to JeVois:
SERIAL.println("setpar serlog None");
SERIAL.println("setpar serout Hard");
You could add a setmapping N in the same way. See http://jevois.org/doc/UserCli.html for all available commands.
Things to be careful about: This assumes that JeVois has already booted up by the time your Arduino sends the command. If you will power both JeVois and the Arduino at the same time, the Arduino will likely boot faster than JeVois. You can then wait until JeVois becomes ready, at which point it will send:
INF READY JEVOIS 1.0
to the serial port. So your Arduino could wait for this to be received, and then send its commands. Note that 1.0 is the JeVois version number and it will change in the future.