You will find that if you install/place all of your files into the poser 5 or poser 6 runtime that you will quickly become confused as to what goes with what because there is usually no continuity between the placed file folders from one library folder to another.

There are any number of ways to organize your runtime.

But first I'll say that I never unzip/install/place any files directly into my runtime until I've inspected it's contents and sorted it out in a way that I feel is organized for my needs.  I have a folder on my desktop called "Unzipped", which is where I unzip/install my poser files first.  Then I go and look into each folder and make sure the files are in proper runtime structure according to that diagram that I linked to earlier. If they aren't in runtime structure, I put them into runtime structure.  I also take the time to rename the unzipped/installed folders (not the folders inside the library folder, but the folders inside the library folders  (character, camera, face,  hair, hand, pose, light, props). Sometimes folders will be deposited directly into the library where the character, camera, props etc folders are.  Those are morph folders.  Don't touch those! 

As for organizing, you can easily use the one runtime that is inside the poser folder.  To do that:

Create sub folders in each of the Character and Poses folders named for each figure (V3, M3, Aiko, David, SP3, etc).

Then when you are installing folders, after you have inspected and sorted the files the way you want them in your "unzipped" folder, then move the runtime to the final destination.  Then go into each of the library folders and move what you just placed there into the proper sub folder.  This way you keep things for each figure in it's own folder for easy locating.  You can further break that figure folder down into sub folders inside by adding more folders called clothing, hair, shoes, jewelery etc.   Doing this you will know that if you are looking for V3 clothing the item will be inside the V3 folder in character, poses.

Hair, Poses and Props can be used across figure, so you can keep those separated by figure if you want, or just by theme/catagory IE: poses, furniture, weapons etc.

I've linked to a tutorial earlier on using multiple external runtimes, so I won't go into that here.

I started off just lumping stuff into my poser 5 runtime, and quickly learned that I couldn't find anything because nothing was named the same in any of the folders. So if I was using Outfit A, I didn't know where in the Pose folder my textures for Outfit A were.   I then sorted my files by figure and used sub folders to further organize the contents, and that worked well.  But I found as my runtime grew that my Poser performance decreased and it took forever to open the program each time.  So then I graduated to a few external runtimes. As I got comfortable with the files and program I gradually added more runtimes.  I have over 40 external runtimes now. Some are:

V3 Clothing
V3 character addons
D3 Clothing
D3 character addons
M3 Clothing
M3 Character addons
SP3 Clothing
SP3 character addons
Aiko
Mil Girls
Hair
Poses
Props
Christmas
Halloween
Valentines
Easter
Lighting
Backgrounds & Envirornments
Angels & Faeries
Mermaids
Vehicals

and others.

I know exactly where every single one of my files is located and can find things very quickly. 

"It is good to see ourselves as others see us. Try as we may, we are never
able to know ourselves fully as we are, especially the evil side of us.
This we can do only if we are not angry with our critics but will take in good
heart whatever they might have to say." - Ghandi