save or SaveAs in Rhino you are making a new file.
.3dm
.3dmbak .
1 - Precedents contains all images, documents related to precedent research.
2 - Site Research contains all drawings, docs, references etc related to site research
3 - CAD holds any CAD blocks used in drawings and model files.
4 - 3D Models holds all your Rhino files
5 - Model Files holds all 3D files you didn't make, but were provided to you.
6 - Illustrator holds you vector graphics from Illustrator / Inkscape.
7 - Indesign holds Indesign files, typically larger layouts, books, boards with many places objects etc.
8 - PDF holds all exported PDF's from other graphics software.
9 - Images holds output from any design software including Photoshop or Gimp.
10 - Administration is useful for professional offices where administrative documents for each project need to be organized.