It sounds like it was operating in "height mode" instead of "altitude mode" meaning that it was using the ~390 m value as the height above ground instead of the absolute elevation to go to above sea level. You can change this setting by going to the Sys Set menu and going to Altitude Offset. There you can change the mode to elevation instead of height.
We pull the highest elevation along the flight path from Google and add the specified AGL value from the Flight Planner to that.
For example: If you specify a survey area that has a hill that is 100 m taller than where you start but want to fly at 70 m AGL, the flight planner will take that into account and add your 70 m to the top of that 100 m. That is a check the ground station software doesn't do and would let you fly right into the hillside... Thanks DJI!
We will be changing the altitudes to be relative to the takeoff point since "height mode" is the default in the software as of 2/2/2015.
NOTE: This only takes ground level into account. Not trees, buildings or any other structures. Setting the flight altitude too low in the presence of tall objects will result in crashing.
This is where using DJI equipment is pretty nice though. They come back to the start point pretty reliably. Certainly better than a bunch of other systems we have heard about...
For the waypoints: You have to know how many way points your controller will allow you to program. The Phantom 2 is 16. If you use a WooKong, it is 50 and the A2 is 200. You just need to take that into account when laying out your flight. We will maybe be adding an equipment selector in the future, but for now, you have to know your hardware's limitations. The AWM file that gets generated can easily be edited with most text editors. Just trim it so it fits.