If we forget about P7 for a minute and go back to P6 which is still my choice at the moment because 7 isn't right then the way mine is set up is different to yours.
My main library is as Poser intended, however what I have done is incluse Sub-folders in each of my main library folders and even sub-folders in sub-folders etc. I don't use any external runtimes and no the initial load time isn't excessive IMO.

As an example, the pose library folder has sub folders called "positional poses" "MAT poses" "animal poses" etc. lots of different ones!  Take that on a bit and the "positional poses" sub-folder also has a sub folder for "V3 poses" "A3 poses" "M3 poses" etc. and likewise the "MAT poses" sub-folder has sub folders like "hair MATS"  "Clothing MATS" "eyeMATS" etc.
Is this making sense??
Navigation is easy by using the little black triangle in your library pallete on the right hand side, do you know the one I mean.
Now back to P7, when it workds correctly I envisage setting up the same system but using the "Collections" tab!
I will try it after backing up my runtime first of course so if it screws it I can get it all back simply enough!!
Hope I haven't confused you, I've done it this way since P5.

Injustice will be avenged.
Cofiwch Dryweryn.