Trouble with Turning Off/Powering Off two systems at once, how should I approach this?
You are making this over complicated by keeping the batteries separate. 

Pick a side and combine them. perhaps the negative side as I have shown below. 







simulate this circuit &ndash; Schematic created using CircuitLab

Or topside like this.







simulate this circuit

Alternative is to use a dual pole relay powered by one of the batteries, but remember the relay will drain that battery faster.







simulate this circuit