Mixing Arduino Firmata with custom code


Is it possible to mix the arduino firmata code with custom code? I’d like to make an application in which arduino is partly OF controlled (if pc is running) but also arduino should check some sensors if the pc is not running, so that it could e.g. start the pc based on some sensor information.
In the firmata setup(function) I found this lines of code

portStatus[0] = B00000011;  // ignore Tx/RX pins  
  portStatus[1] = B11000000;  // ignore 14/15 pins   
  portStatus[2] = B00000000;  

So is it possible to ignore some more digital pins and use them just as i’d use them in an “normal” arduino sketch, e.g. I write my sensor/button/whaterver function which uses this (firmata)-ignored pins as inputs/outputs and everything else runs the same?
By the way: if the answer is “yes, you can”, could someone explain, how I read the above code or how I’d calculate the binary number for a pin I’d like to ignore?

Thank you and regards,