Circuit safety -> Preventing smoke through accidental connection of battery voltages
All you're doing is reading the voltage?  In that case why not just slap in extremely low-current fuses?  That's a kind of hack-y solution but it might do for your purposes.  Though I see you say this is actually connected to a motor as well, so almost certainly no then.

Another option is that it looks like the connectors are 0.1" spaced, and you could put on a single 5 pin 0.1" header, and just tell them to always plug it in in a certain orientation (you wouldn't get the polarization protection from the header shroud/guide).  Then you wouldn't have to worry about multiple batteries plugged in at once, but you would have to worry about users plugging the connector in backwards.  But you could protect that by having a reverse-polarity protection diode which shorts ground to Vin in the case of a reverse polarization plug.  This has the disadvantage that if someone plugs it in backwards they'll get an extremely hot diode, but it should save the rest of the electronics. You could put an LED that says ERROR_REMOVE_BATTERY which turns on if they plug it in backwards and hope that people would notice it?

This is the problem of how idiot-proof do you really want to make your system?  Because no matter what you do the universe can throw a bigger idiot at the problem.  I think plugging in multiple batteries simultaneously seems unlikely, but that's just me.

If all you're looking for is dip-switch configurations to prevent multiple batteries from being connected you should probably be aware that if these switches have to handle the current coming from the battery then you should expect to pay a lot for them (like $10 per switch at least), and the answer is probably just to have either the ground connections or the positive connections disconnected unless a switch is thrown, one for each battery.  This is simple but similarly prone to error (probably more prone to error than just not connecting multiple batteries simultaneously).

Hope that enormous ramble helps somehow.  Good luck figuring it out!