Pulling power off a battery stack at different voltages
Your scheme of tapping off the batteries at different points will work.  However nothing is for free.  The batteries used in both the 6V circuit (let's call them Bat1) and the 12V circuit (call them Bat2) will see more power drain than the two used for just the 12V circuit.

The problem arises when you want to recharge them in series.  Bat2 which will have more energy than Bat1 will raise the voltage of Bat1 + Bat2 faster than normal.  Often this causes the charger to back off the current, which ends up leaving Bat1 undercharged.  They cycle can worsen over multiple uses leaving Bat1 either undercharged or overcharging Bat2.

This is why most electronics derive the power they need from the batteries keeping the charge and discharge paths identical.

You could choose either to boost the 6V or regulate the 12V.  Typically the decision is made by which circuit needs the most power delivered to it.  In your example if the motors take 2x more current than the rest of the design, then it would make sense to optimize the delivery of the supply to the motors.  If everything is about equal, then it comes down to looking at the cost/efficiency of linear regulation (less EMI and simpler) versus boosting it (noisier and more components).