Well, while one can create 3D maps in Celestia, it is true that the overhead of creating something that looks like what you want can be a bit overwhelming. I often do it by using Anim8or to create a 3d model of the structure that I want, for example.

Using a 3D design program by itself might be another option. I like Anim8or but some prefer Blender or others.

An example of a 3D map shown in Celestia can be seen at https://www.youtube.com/watch?v=SLOx-zZcho8

It shows travel routes between stars.