LVD solution with low power indication
I'll hazard a guess that this Over-Discharge Protection circuit proposed by Russell McMahon may fit your needs. Its schematic is below.



I think you can use it in the following manner:


Place your batteries between GROUND (the horizontal wire on the bottom) and V_battery;
Feed your step-up converter off of the O-DP circuit's Vout (linking it also to GROUND);
Wire one of your Arduino's digital outputs to HIGH to run;
Link one of your Arduino's analog inputs to Vout so you can measure the battery voltage. Add a voltage divider if Vout can be higher than your MCU ADC maximum voltage.
When you press the Go! button, your MCU must set the digital output linked to HIGH to run to HIGH;
When battery is low, just set HIGH to run to LOW. That will turn off the circuit.


Just make sure you don't link any of your MCU pins directly to the battery, or else these will power your MCU through the protection diodes. That will bypass the O-DP circuit and may damage your MCU.

Note that there may be a voltage drop up to 0.7V between V_battery and Vout because of the BC327 transistor depending on the current you draw from the circuit.