Set first level protection to 1V below current voltage. Ignore 2nd level for now.
Fly until red light
Land, measure battery voltage
Subtract what you set as level 1 voltage from your measured voltage. This is your voltage drop. Eg, You set 15.8V as your level 1 voltage, you landed and then measured 16.3V. 0.5V is your voltage drop.
To set your actual level 1 voltage after this involves flying and measuring how much charge you are putting back in to your cells. Start with 3.7V per cell (14.4V for 4S and 11.1V for 3S) then fly until red, land, charge, measure how much you put back. If you're putting back less than 80%, drop the voltage by 0.1 (more than 80% add 0.1V) and repeat until you're putting 80% back in to your cells.
For level 2, set at 3.3V to 3.5V per cell. This is for auto land but you should never get to this or you will shaft your batteries. I actually have mine set way low as I don't want the copter to auto-land and would rather trash a lipo but fly the copter home than have it auto-land in a field or lake.