What I do is this:
Build up whatever EMPTY VEHICLES or OBJECTS I want to make a base or whatever using the 3D view.
Then I place a CENTER, a GROUP and a single UNIT anywhere (this unit won't survive the conversion).
Save the mission.
Then I use this tool
to convert the mission to a 2D mission. Then I swap to the 2D editor and MERGE that new 2D mission with my real mission and get the base I laid out. The single unit I put down won't be there though, that was just so i could save.