When I run the road runner Gcode, my spindle on/off button lights up requiring me to click it before the machine will take off, causing me to miss steps. I dont control my spindle with Mach3 , I use a router mounted and wired separately. How do I turn this function off?

Second question is when I reference my Z it goes up to the home switch, but when I run the same Gcode file the Z goes up one inch instead of down one inch simulating cutting. The only way I have found to make it go down to cut is to reference to the down switch. Is this the right thing to do?

Thanks