Why do you need to pause the program?
For testing purposes?
If so, you can code a switch, when closed allows the code to execute, when released if stops.
Code:
if ((autonomous_mode = 0) || (AUTON_SWITCH = 1))
{
execute auton code
}
Or something like that. (I don't have my code in front of me.

AUTO_SWITCH - is an alias to one of the O/I joystick triggers for testing only. Make sure to remove it before comp.
Phil