Yes, you need to calibrate the power module for VOLTAGE and CURRENT. The procedure out lined here: Power Module Configuration requires using a watt meter to calibrate current, but I have a much safer and more accurate way...
The basic process is you take a fresh battery and make a flight of 5 minutes or so, land, disarm and unplug the battery. Charge the battery and record the mAh charged. We will call this number "CHARGED_MAH"
Now take a look at the flight logs and find the total current used. We will call this number "LOGGED_MAH".
Next look at the BATT_AMP_PERVOLT parameter and record that number (by default its something like 17...). We will call this number "OLD_AMP_PERVOLT"
So, let's say LOGGED_MAH was 1300Mah, CHARGED_MAH was 1500mAh, and OLD_AMP_PERVOLT was 17.
We can use this formula:
NEW_AMP_VOLT = (OLD_AMP_VOLT x CHARGED_MAH) / LOGGED_MAH
NEW_AMP_VOLT = (17 x 1500) / 1300
NEW_AMP_VOLT = 25,500 / 1300
NEW_AMP_VOLT = 19.61
Set BAT_AMP_VOLT to 19.61 and click "Write Params"
Take a fresh battery and make another 5 minute flight.
After one or two iterations you should be well within +- 200mAh..
For the low voltage warning, set it to something just above 3.2 volts x the number of cells and set the reserve current to 20% of the battery capacity. For a 3S 3000mAH battery this would be 9.6V and 600mAh respectively.
The reason for using these numbers is you want the low battery fail safe to always trigger on low capacity and never on low voltage.
I do this with my APM quad and my Pixhawk hex, and the end of flight at rest cell voltages are never below 3.7 volts.