The 3D editor isn't really complete. Missions made with it can ONLY be edited by the 3D editor. You can't go into 3D, put stuff down, then try to edit it in 2D.
You either need to convert the mission (keeping only empty objects and vehicles) or edit scripts to then run them in missions made with the 2D, but as you discovered in your other thread you cannot see these scripted objects or units in the editor.
Best thing to do is simply use the 3D editor to plan out bases and empty vehicles, convert them using a tool, merge that with your 2D map in the 2D editor then add units. Search around for the convert tool. :)