Battery voltage select and ADC measurement (OpAmp + uC)
Since the jumpers have to be set manually, a simple solution might be to use a second jumper that indicates the selected gain to the microcontroller. So the user have to set two jumpers to identical positions. Or just use a rotary switch with two poles and three positions (e.g.: SS-10-23NPE).

A completely different approach would be to implement a autoranging function, where the microcontroller selects the gain factor automatically. Just use a small analog switch that will be controlled by the microcontroller.  Now it is possible to auto gain the input signal: start with the lowest gain factor and work your way up just one step before saturation of the ADC input would occur. If neccessary protect the ADC input from overvoltage: just add a clamping zehner or TVS diode (important: low leakage current!) to the output of the amplifier.