Multiple serial monitors with the same arduino mega
Use an USB to TTL Serial adapter. Wire it to one of the RX/TX pin pairs and in code use the corresponding Serial object Serial1, Serial2 or Serial3. Don't forget to wire Ground. 

You can use some terminal program or Serial Monitor in Arduino IDE to communicate over the adapter. You can open a second instance of the Arduino IDE by starting it with the Desktop or menu shortcut. In this instance you can select a different port then the sketch upload port.