And hopefully, this gives you and some of the other new guys some insight into how the system works.
Rep-G does 2 things-helps create gcode using skeinforge ( the actual commands used in printing as a file). Replicator-G also is used to communicate via serial port to the motherboard and most importantly, the firmware command interpreter. This portion of the firmware takes the gcode commands and does something with them, translating them into pulses for the stepper drivers.
When you send a command from the rep-g control panel-it's the same as opening hyperterminal, and sending text across the serial port. Rep-G is not controlling the bot, the firmware is upon reciept of valid commands from the serial port. All rep-g does is send text-thus why indicating endstops has little to no effect, in fact the only thing is does is change the homing buttons in rep-g control panel. When you generate gcode- it appends the start and end gcode in the profile chosen and ignores everything else. So the ONLY place affected is the control panel.