I have 3x 18650s wired in a series, connected to the BMS seen here. The two outputs of the BMS are wired to a MOSFET that drops the voltage from 12 to 5, in order to power an Arduino Trinket Pro.
During prototyping I was using your basic DC jack to connect to the Arduino and charge the battery pack. However with the 3D printed part I have this all in I am using a different battery contact to connect the battery pack and Arduino.
Now I am needing to find a different way to charge the battery pack, preferably through a micro USB or USB C charging port, like you see on portable power packs.
I've picked up the TP4056, seen here, and the USB C version. My question is can I / would it be a good idea to splice off of the BMS outputs, and insert a diode into the connection between the battery contact that connects to the Arduino and a diode into where the TP4056 runs.
The first time I had tried it with a standard micro USB port, no diodes, which heated up very quickly.
Or, would I be better off just running the TP4056 straight to the positive and negative terminals on the pack itself, bypassing the USB. 
Best Answer
Three 18650 lithium battery cells will be 12.6V when fully charged. The TP4056 is made to charge one cell or a few paralleled cells to 4.2V so it will not charge your cells that are in series. A Mosfet by itself will not regulate the 12.6V down to 5V.