The "Charge Pump" is an actual device that can recognize the 5khz signal output by Mach3. It is wired into the outputs per the Ports and Pins using one of the output pins. It runs on 5 volts, and when it sees the signal, it operates a relay. CNC4PC sells such a device, and also some of the BB have this capability built in.
The CNC4PC Charge Pump also has a red LED that turns on when the signal is received, making setting it up much easier.
As I said in a previous post, you can select whether the "Charge Pump" stays on during an Estop. The Charge Pump relay is commonly used to control the EN "enable" signal on the drivers, thus keeping the machine in a no-motion state until the Mach3 program is loaded, and has control over the Drivers.
It is not necessary to wire the drivers power into the Estop switch, as the Estop state is seen by Mach3 as a "no steps output allowed" condition, and the motors cannot move.
The Estop is an "Input" signal to the Mach3 program, and the "Charge Pump" signal is an output signal by the Mach3 program. They are two entirely different things in the operation of the Mach3 program operation.
Thus, the "Charge Pump ON in Estop" allows the drivers to have power, holding torque and position during the Estop condition, since the Charge Pump is in control of the 5v. Enable signal to the Drivers. This assures the machine current position will not become altered due to a power-down state of the drivers.
Most stepping motors are 200 full pulses per revolution, but micro stepping settings break this single magnetic pulse into more "partial positions" in the magnetic field. If your machine is put into Estop, and the motor happens to be in a "partial step position" due to micro stepping, a full Driver Power Off state will lose this partial state position. When power comes back ON, to the Driver, the motor will assume the closest full step position, and not be in the same position as before the Estop.
The Charge Pump is also known as a "Safety Charge Pump", due to it's function in the machine Start-Up. If you do not have a Charge Pump wired into your machine, it will still function properly as long as the Driver power is not disabled during an Estop. Since you don't have an actual Charge Pump on your machine, the General Config setting does not apply to your machine.