Someone here might have a better way to calculate this offset, but here's how I do it:
1. Select a flight that is either on the ground or that recently took off from the runway that I detect flights from.
2. When the aircraft shows on the ground or the trail shows originating from the runway, then open the 3D View settings window
3. Almost always, the flights show too high (they might be too low, but I rarely see this case), make a guess in the offsets to bring them down. I start with -1000 (then check 'apply offset' and click 'Apply'. In ~5 seconds, you should see the aircraft icons/trails shift down 1000ft. If the trail or aircraft goes under the earth surface, then that's too much, try bringing it up to -750. A bit of tweaking here usually results in a decent guess. From my experience this stays pretty consistent for a few days, but it is probably location dependent.
Until we can figure out how to calculate this offset precisely, it's only there to make rough guess offsets. Hopefully this helps.
