So you are saying have the arduino be powered by which ever source and control which source is powering it? That sounds like it could fail at some point and the arduino would need powered at all times.
Yes, I will have a master switch to shutoff the project. I am hoping to keep the project component separate from the power, the power supplies (car and lipo) only supply power.
How about a little more detail. The project will run off the lipo most of the time. Most of the time I will just shut it off while the car is running (not legal to have this on while driving on public roads). So while I am driving why not have the car charge the battery is what I am thinking. However, if parked at a show and the car is running I figure why waste the lipo battery when the alternator is running also.