The method that works for your project will likely depend on the specifics of your project, I think: Does your scene use heightmaps, modelled geometry, procedurally-generated parts or some other type of terrain? Are your objects intended to be placed manually or procedurally, and what requirements does placement have (for example, do your objects have any properties that should be set)?
In general, for a fairly large scene, you might consider using your 3D-modelling tool to arrange your scene, perhaps some code in your game that reads exported tags in order to handle custom properties, or perhaps one of the editors that have been posted on the forum at various times, such as this one or this one, as appropriate to your project.