As far as I know the majority of bases, especially those used in the setPos Comp were made by (you guessed it) setPosing a load of objects.
You can probably just click and manipulate ground-level objects in editor, but for stacking objects or placing them on top of buildings you need setPos.
The command is "obj1 setpos [getPos obj1 select 0, getPos obj1 select 1, 5]". Which goes in the "Initialization" field of the object when in the editor.
"Obj1" is the Name of the object, the first two fields of the Array are the x and y coordinates and the last one is the height above the ground (in this case 5).
More
here.
Hope this helps, better wait for some more insight on this subject first though. I'm learning as well.
EDIT: If you want me to go into more detail, I'll be happy to write you a "mini-tutorial" via PM.