The small subs are not designed to generate their own power. They charge the batteries by docking to a sub that is designed to transfer power to the docking ports. The only stable method to generate power is to put in a reactor and scale it down to fit in the shuttle and reduce power output to match...

The fact that it is exploding the moment you turn on the reactor suggests that you are pumping too much power through the grid. J-boxes overload if you push 2x the Power needed to satisfy the Load. What is most likely happening is that you created a short circuit by adding the second engine without ...