Motor Control System for LGB Trains
Use a buck converter to avoid the power loss when dropping the voltage down. Dimension Engineering has some good modules, and an excellent introduction here.
It depends on your specific regulator, but the easiest thing to do is to put some capacitors on both the motor power supply and the sensitive electronics rails.
A fuse is the easiest method of protection, but requires that you replace it every time the rails are shorted. A DC breaker will protect your batteries and is resettable after a short.