It depends on what type of batteries they are. For example, two 9V batteries would need to be connected in series by taking two snap-ons, soldering the red wire of one to the black wire of the other, and just use the remaining two wires normally. If they are two AAs or AAAs, you can find a battery holder at Radioshack, as well as the snap-ons for the 9Vs. If you have two batteries of different types, however, you're asking for bad things. But in this case, you can use one battery for the motors and one for the controller. A 9v works good for the microcontroller with a capacitor and a voltage regulator. A battery pack of 4 AAs is good for the motors with another capacitor.