I have a single kicad directory with my lib stuff, projects for v6 (which will be archived soon), projects for the upcoming v7 stuff, like this:
~/kicad/mylib
~/kicad/mylib/3dmodels
~/kicad/mylib/database
~/kicad/mylib/footprints
~/kicad/mylib/symbols
~/kicad/projects-v6
~/kicad/projects-v6/project1…
~/kicad/projects-v7
~/kicad/projects-v7/nutherproject…
I simply use Preferences/Manage-Symbol-Libraries to add my .kicad_sym lib and turn off the others. Likewise, I use Preferences/Manage-Footprint-Libraries to add my footprint folder and turn off the others. The 3d models are linked in each footprint file. The database is a new and fun work in progress.