To clarify your other questions, "Ground" is generally just a point on the circuit that most other things are referenced off. you pick it at a convienient point and so be it,
Your circuit does not have to connect battery1 + to Battery2 -, Instead i would strongly recommend it is done outside of your circuit, If someone miswires something, you could have many hundreds of amps across your PCB.
For such a circuit I would say it could easily be done on 2 layers, assuming your not doing much more,
In kicad I would probably approach this design by copying the first batteries design, updating battery1 to battery2 on the designators, running the annotation wizard to assign new ID's to the new parts, and have them function as 2 independant circuits on the same PCB with no interconnections.
In almost all beginner boards I would say avoid blind or buried Via's, simply because it costs more, (another hole plating pass)