One thing that I did read is that somewhere I should define the port on the Arduino for the connection with the bluetooth? I'm using Linux (11.10) and the Arduino is defined on.../ACM0 but other than that I don't know where to define a specific port for the Arduino to talk to the bluetooth.
I'm not following this. The Linux box shouldn't be connected to the USB port on your Uno while you are using the RN 42. So (unless I am missing something) the port setup on your Linux box would be irrelevant.
My suggestion would be to use a stripped-down sketch that does nothing more than flash the LED briefly every time a character is read from Serial. You might also want to try to establish communication with the Uno/R42 through a BT connection to your Linux box to see if the problem maybe lies with the Android app.