It's generally not a good thing to have the ESC warn you when the cell is low...by that point it's usually lower than the recommended 3.7v/cell, and the whole airplane in the air running out of power thing.
Best way to do it is use a timer if your radio as one, even a simple kitchen timer can work if you remember to start it. Fly for a set time, such as 5 minutes, check voltage, fly for 7 minutes, check voltage, ect. The goal is to set the timer to where you reliably land with the battery pack at about 3.7v per cell, or 11.1v on your 3S battery. The battery will be a little lower when you first land, they recover some as they sit and cool down after use, so don't worry if you see 3.65v at first, for example.
This website helped me learn all about proper care and feeding of my lipo batteries. Check out the other articles concerning charging, chargers, power supplies, and parallel charging if you have any other questions, very informative.