Hi.
Put this in the init line of the unit:
this setpos [getpos this select 0, getpos this select 1, 10]
This will position the unit 10 meters above original level. In the air if no building is present. Try adjusting that last number to fit your purposes.
In ArmA units will sometimes climb ladders automatically, if the waypoint is placed correctly on the building. Try this to.
Some buildings (the big hotel for example) has building position numbers that units can go to. Place the waypoint on top of the buildings name in the editor, open up the waypoint for editing and choose house position. Sometimes these building poition numbers also include the roof.
Cheers
Laggy