Hi Mathew -- Welcome to the pit. The approach I use is to create a "Folder" ("Directory" in my terminology) for each Project. My Project Directory will have SubDirectories of: Installation (what many call "Top Assembly"), Standard Hardware, Purchased Components, Project PDF's, and Project Documentation. My reasoning behind the Standard Hardware and Purchased Component directories is that (say) "SAE Grade 5 0-5000-20UNRF X 1-500 Long Hex Head Cap Screw components used "across the Project" need only a single Model to create all "XXXX" places where they are used in the Project. This makes it simple to create a full "Project Archive."
Within the Installation Directory will be SubDirectories for Major SubAssemblies (as many as needed), Common Fabricated Parts, Common SubAssemblies, and Part Lists. Wirhin each Major SubAssembly (Sub)Directory will be SubDirectories for Major Sub-SubAssemblies and Minor Sub-SubAssemblies as well as a Directory for "Parts common only within this Major SubAssembly. Etc. The PDF's of the Drawings get stored
Thus at (say) Project Revision D I can "7-zip" the Installation Directory (and all sub-directories therein) in an Archive that I can name as (say) "Project -- Rev Dp01 -- 20200422A" and know that it documents the first preliminary ("p01") version of Rev D as the first ("A") version of the 22nd of April 2020. This is almost simple! -- Lew