As flygirl said, except of course it's fine to use the limit function. Remember, it does have two stages but everyone gets obsessed with the second one.
For first stage I would set something like 10.9V. When you see the yellow flashing light (depending on what system you have) it's time to land. I set the second one really ridiculously low, like 9.9v. It is just for super emergencies like a failing lipo.
When you land and unplug the lipo the voltage should read something like 3.8v per cell (more like 15 minutes after you land as the lipo sometimes needs a bit of time to bounce back).
Using a timer is essential during a flight. You'll get to know how long you can fly for and how wind shortens flight times etc. Use this and the first stage alarm to time your flights along with how many mah you are putting back into your lipo when charging.