Hi,
We just finished our smartphone controlled arduino car, but we got some problems with the low voltage alert which should warn us when the 2-cell LiPo accu voltage sinks under a specific amount. For that we connected the middle pin of the balancer connection (which delivers 4.1 to 3.3 V = Voltage of 1 cell) to the A0 analog input. The alert works fine, but when the main switch is turned off, the arduino is obviously still powered by the analog input (See wiring diagram attached). We wondered if this effect is damaging the arduino, and how it could be avoided.
Maybe there is current because with these accus a circuit is created with the positive OR negative power pin and the middle balancer connection.
Please take your time and think about it, the diagram may help you (I hope so :~). Thank you! 
We wondered if this effect is damaging the arduino,
Yes it is called parasitic powering and can cause all sorts of problems.
Basically you should never supply power to the pin of an unpowered chip no matter what it is.
One solution is to connect the pin through a relay's contacts so that when the power is removed so is the monitoring voltage.
the diagram may help you
No the diagram is appalling, not only is it badly drawn it is so big as to be useless when you click on it. Please read the how to use the forum sticky.