Measuring potential between two pins below ground
An ordinary inverting amplifier does this for you. Because of the virtual earth effect, the inputs do not go below 0. Actually most opamps whose inputs work to zero, will work to 0.5V below ground i.e. until input protect diodes start to conduct







simulate this circuit &ndash; Schematic created using CircuitLab

Using a low-drift, low offset amplifier simplifies life, but you can use a port pin to zero the amplifier and calibrate offset and drift out in software. Again, as long as the voltage is clear of 1 diode drop, output ports work below zero - they are just an NFet