I guess I'll let my ignorance shine here, but..... the controller's wired in between panels and batteries, both have varying degrees of volts and amps the controller interprets. I presume how big the differences are are what the controller uses to make it's adjustments to do it's job. Bottom line is that electricity is "coming at" (for lack of proper term) the controller from both sides. Granted even with small voltage differences things should move towards the battery but disconnecting either one first still leaves the controller hooked up to power. What's it matter whether it's panels or battery first?