Is this a Litchi specific question? I am yet to use Litchi but in UAV parlance, "above ground" means the altitude of the AC with respect to the take-off point i.e. the altitude the AC has risen from the ground where it took off from. It is abbreviated as AGL altitude. When we speak of altitude, it is important to specify this because GPS data usually gives the altitude above sea level or ASL altitude.
So I am guessing if you do not check the "Above ground" checkbox, the value you enter will be inferred as ASL altitude. But I may be completely wrong here as I have never used Litchi or any 3rd party app. Hopefully the other pilots will correct me.