CrossRoads:
I would recommend a switching regulator for the 5V. Otherwise you're just wasting a lot of battery charge as heat in the regulator.
Say the Mega and whatever LEDs, etc you have connected need 350mA of current.
Power = Voltage x Current.
(12V in - 5V out) x .35A = power dissipated as heat = 2.45W. That regulator will be Hot! and may go into thermal shutdown.
Thanks,
I decided to use 2 seperate Regulattor circuitry. 7805 for arduino and 7809 for Dc motors.