Answer to what a command does when the robot is disabled is in the Javadoc for one of the methods of the Command class:
http://first.wpi.edu/FRC/roborio/rel...f269d3ec63faa8
As long as you have a call to run the Scheduler in DisabledPeriodic it will cancel any commands that you haven't run the above method on, run the commands you have (without motors moving) and continue to poll any OI stuff you have mapped and schedule appropriate commands (assuming they are set to run when disabled).