In the Free Flight mode I don't know. But in the editor you can type this in the initialization box to set the chopper altitude.
Code:
this setpos [getpos this select 0, getpos this select 1, +1]
I invit you to follow this guide 
http://takeonthegame.com/take-on-editing/
---------- Post added at 15:45 ---------- Previous post was at 15:26 ----------
- Place a empty helicopter on the map. Name it "chopper"
- Place a player on the map. In the init box type "this moveInDriver chopper"
In you want the engine to be turned on change the "state" of the chopper to "fly". Then you can set the altitude by typing this line in the init box of the chopper.
Code:
this setpos [getpos this select 0, getpos this select 1, +0]