How would I combine several projects?

Okay, so I am trying to package a Maratis Starter pack, which includes scripts and objects from various projects. However, I don't just want to drop all meshes in the meshes folder, and all maps in the maps folder etc. I wanted it to be a bit more organized.

However again, when I create a new directory, I have to edit the mesh files to point to the correct folders, and all corresponding maps.

I am wondering if the .level files of the projects are all I need to separate the various scenes (as long as the meshes and maps and scripts are in their correct place.)