If the layout of the game is simple enough and there are not many objects, it is a suitable way to position everything from the game code, just working out the coordinate values by trial-and-error. With larger worlds, this does not work any more.
Some people use the 3D World Studio program (sold by TGC on this web site) or even a 3D modelling application to build the entire world. Then either export it as one huge object (not very good for performance reasons) or use a more sophisticated loader. There is one Dark GDK loader for 3D World Studio files, for example, which can interpret all details in the file format, from objects to lighting. I had the link somewhere, can't find it at the moment. The project has a thread on this forum.
You can also write your own world editor. I started to write one which was (still is) intended to be made available for the community, but unfortunately it is progressing at the speed of about one code line per month, so I don't know when it will be in beta stage. From time to time, world editors may pop up on the forum as well, for example here is a very promising 3D editor in WIP stage, unfortunately it seems there are only screenshots yet, no demo:
http://forum.thegamecreators.com/?m=forum_view&t=159294&b=8
I'll try to find the link to that 3DWS loader as well and post it later but it's useful only if you intend to use that software.