You can have the batteries in the car or out. Its easier for me to have them in the car and batteries soldered in so i dont have to worry about putting them in the car connecting the battery up and rushing out on the track. As long as the batteries dont short out you'll be ok.
When you have the wires connected you can charge them as well. but just make sure the esc isnt on.
If you have any other questions go ahead and ask. If you need more info that i didnt provide tell me. Hope this helps.