In broad terms, you should always use them. It is simply something that cannot hurt you to do, but could cause serious problems to ignore.
You have probably not seen any major problems with your batteries because they are placed relatively close to your chips and because they have an internal resistance to snub higher frequency signals.
This could still cause power concerns in higher frequency signals. If a Microcontroller runs at 20MHz then you are having 20e6 pulses of current pulled per second. This may not seem like a big issues, but when enough inputs change at once you may cause ground bounce or many similar problems that come with high inductance paths to ground.
The wikipedia article has some background if it helps.
Little extra on decoupling capacitor terminology
The job of a decoupling capacitor is to "decouple" your devices power draw from the rest of the circuit. If a decoupling capacitor does its job you will only measure a DC power draw. They remove the AC wave.
There are different terms for decoupling capacitors.
The bulk capacitors act as large power sources that can supply power for periods of time, these are required for functionality. Without a bulk filter cap you will have to have time dependent current as your chip pulls power on it's cycle.
Bypass capacitors are often of lower value and are designed to terminate higher frequencies. As frequency reduces your impedance decreases for capacitors. A smaller value capacitor has a higher impedance. These small capacitors are the backbone of terminating higher frequency waves.
Decade capacitors are another term for bypass caps but the name implies more. If your bulk filter cap is .1uF then your decade caps will be .01uF and .001 and even .0001uF depending on what you are doing. Normally I only see 1 decade cap, but I have had to use 2 or 3 before.
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).
Best Answer
Yes, you are better off getting a dc to dc converter to convert the 36V to 18V to run the 18V motors.
This is because you will cause an imbalance between the two batteries by using only one to run the 2 18V motors.
You could, possibly, consider running 1 18V motor on each battery but that may mean control and wiring issues and the possibility someone makes a wrong connection... Lots of sparks or a fire then.