About file organization/workflow

Project has the groundwork laid down, its gotten to the point to start building levels, and customizing the bad guys. This involves importing a lot of meshes, animations, materials etc… about 50G worth… Anytime I import all new assets maintain their imported file structure thus really wrecking my projects files.

Is it beneficial to start these items in a separate project, build them there, then import the finished modular level into the main project? that way anything unused is not bloating up file size?

Whats the general workflow? Work modular and import, or just toss All assets into the main project and pray that it sorts out in the end?