How to use 18650 batteries and increase voltage from 3.7v to 12v
tl; dr: consider a 4s RC hobby pack+charger solution. All the problems are solved for you.
I can't recommend 3s + boost converter for running a high-current motor load as this adds losses and increases the current demand on the battery pack, shortening its life. Using 4 cells (4s) is better, and as it so happens this is a popular pack for RC cars anyway. Your 12V motors will do fine with it.
Also, by getting a pre-made 4s RC pack it will have over- and under-charge protection built in. This is important for safety and preserving the battery.
Finally, you have your choice of chargers which can charge your 4s pack up to 14.8V. The intelligent ones can be set to get the best performance and life out of your battery.