Short answer is: when you run the program in netbeans it will download the executable to the crio, reboot the crio and start your program. Then use the driver station to set the game mode (Autonomous or teleop) then start the match. This will start you program running in the crio at either the start of teleop or Autonomous.
I highly recommend you learn how to attach the debugger as soon as possible because it will save you many hours that would otherwise be wasted watching the crio reboot
