Hey, my answer is short because I'm only a year into using Poser, but just hit the wall with the same problem this week.  But the problem you have seems to be shared by many.  I kept thinking, I must be doing something wrong because I just didn't think Curious Labs would have the program doing installs all over the place, but they must have their reasons because that's what happens to most users after some time.  I gave up a couple of days ago and bought PBooost II off of this site.  It was the best move I could make.  I fixed all of my filing problems in one evening.  I don't think that there is a right way or best way to organize as it is going to vary with the content you use and what you do with Poser.  The Pbooost II just gives you a very clear understanding of a method to the madness which I think is the critical first step.  I just took everything and put it into the default folders to start off with (figures, poses, hair, props, etc. - the program sets that up for you) and then I broke it down to 1. Characters 2. Non-human Characters 3. Things  within each default.  I then broke them down further in each of these.  That worked really well for me.

Good luck!

 

Tapper