Well, its not exactly clear what your asking in your first question but I'll try.....er.....turrets are backwards on the bottom of ships because they are upside-down. Think of it as the turret being rotated 180 degrees from its usual orientation. (OK, I know that was probably no help)
As for docking point problems, I presume you are talking about docking points that you have made? Have you defined paths for the docking points?
Extra things for turret paths?
What have you got so far?
A turret path should have the corresponding turret sub-object as its parent, vertices, and a radius for each vertex.
As for your icon problems, well, no idea.
Well, I think I can safely say I was no help at all, so I think I'll shut up now. Sorry.