Reading differential signals
how I'm supposed to read the differential voltage shown with the blue
indicators

Use an op-amp configured as a differential amplifier: -

Picture from here.
You may need to create a small negative voltage for the op-amp negative rail or, if you choose your op-amp carefully (inputs capable of working close to 0 volts on your schematic), you should be good to go.
Another thing to think about is the frequency of the ripple you are trying to measure; because your circuit is a boost converter, it will be running at (probably) several tens of kHz so, choose an op-amp with reasonable bandwidth in order to measure your signal without high frequency attenuation.
If you need the ripple voltage centred at some DC offset suitable for your ADC, the ground connection of resistor \$R_g\$ above can be changed to that offset voltage because \$V_{out}\$ is referenced to that voltage.