You can power every component of your project with a separate battery if you want. I could have one battery for my AVR, one for my sharp IR distance sensor, one for each servo, one for each motor, and one for my receiver. Just make sure that the parts that communicate with each other via voltages share a common ground, and be careful not to hook things up wrong (e.g. in a way that would short two different voltages together, such as the 5 V terminal of one battery to the 9 V terminal of another when they share a common ground).