Don't you hate it when you have to put the work "almost" in your log?
I updated the picture of the layout. You should be able to see now where I'm going with this.
1. Attach the Board Power FET's control to an MCU I/O. Choose a good pin.
2. Put solderstop-less polygon on the main battery and GND traces, so that I can reinforce those with copper strands after the board is fabbed.
3. Add debug LEDs.
I know that blinking LEDs are bad for the eyesight and sanity of anyone later admiring my handiwork, but they make such wonderful debugging interfaces. ...Alternatively, I could add some more headers to any free pins. Headers conneced to spare I/O pins tend to buffer against screw-ups.