Mike, in mach on your screen you will see cycle start, Feed hold, stop, and Reset.
Stop is similar to EStop. it stops except it stops the motion without shutting things down It if used by itself will lose steps. RESET is ESTOP. Feed hold will run a snort distance as it already has lines in the buffer, then it stops motion with out losing steps. at that time then you can press stop if needed to fix a problem.
When you run a tool path it finishes up and parks at X0, Y0, Z + whatever above that is set. It then stops the program and the machine, all while keeping the steppers in a hold mode. It is then, if you have a router that you would turn the router off and change the end mill. The same would apply if your spindle is not MACH controlled. You will turn off the spindle and change the end mill. Then you load the new tool path, reset Z zero for the new end mill by jogging over to the place you use for Z zero setting for that job and rezero Z only, since X and Y should not have changed , raise endmill from work in Jog mode, then Turn on the router spindle and then press cycle start. When done again, wash and repeat.
Mike