You can split any project in several parts. Then in Artlantis use the "Merge Geometry from File…" command available from the "File" menu.
E.g. in SketchUp I have a material placed on facets named "Concrete". I have 2 different layers with facets with the same material name. One layer is visible the other not. I export to ATL.
I change the layer making the one visible and the other one invisible, then export to ATL.
In Artlantis I open one file then I merge the second file, as the material have the same name from the 1st file to the 2d one in the material list the names are displayed 2 times. So I can put a different color a Shader on them.