Sv-06 plus laser

Ok I have an 06 plus, I finally got around to installing the 40w laser.I havent had a chance to try it yet because i am printing other stuff but i have a question. How does the printer know which will be used, the hot end or the laser? I have just skimmed over the program Inkscape but havent really done anything with it yet. I was printing a Pla milling plate for my new Sherline milling machine and while it was printing, the laser was engraving my build plate at the same time!. It didnt ruin it or anything but it did leave marks on my build plate.Any assistance would be appreciated.