We are making a electric vehicle that runs on a 100v system. We have a second 12v battery that powers some power monitoring circuit that runs constantly. When the 12v battery is low it opens a mosfet (Q1) that turns on the 100v-12v DC-DC converter, due to the high quiescent current of the DC-DC converter it will usually be off and only turn on when the 12v battery is low.
The problem is that if both the 12v battery and the 100v battery were out of power, the 12v circuit would stay dead even if the 96v voltage battery was charged. Because of this I changed the mosfet to a P-channel. My question is do I tie the gate pin on Q1 to ground and use a N-Channel mosfet to connected to the high voltage battery to provide the necessary voltage to turn off Q1 mosfet. The mosfet I am looking at has a max Vgs voltage of 12v. It seems by doing this I am frying something though I don't know how to fix it. Any advice would be greatly appreciated

 

That puts way too much voltage on the gate, which probably has a spec of -20v or so. You could use a simple resistive voltage divider to limit it at the gate.

Put the N channel after R2 and use another resistor from the high voltage to R2 and the gate of the P channel.

 

Why dont you use a relay with a set of N.C contacts driven by the Atmega instead.