To have one runtime with subfolders all you have to do is create whatever subfolders you want inside the default library folders.

For example if you want to separate V3 clothing from M3 clothing you would go to the character and pose and props folders and create subfolders called "V3 Clothing" or "M3 Clothing" and from there create further subfolders inside those by the name of the outfit.  So for example you might have a path like this:

Poser6/runtime/libraries/character/V3 Clothing/Morphing Fantasy Dress
Poser6/runtime/libraries/poses/V3 Clothing/Morphing Fantasy Dress

You can create yet another layer of subfolders inside those to have something like this:

Poser6/runtime/libraries/poses/V3 Clothing/Morphing Fantasy Dress/Jane Smith Textures (where Jane Smith is a merchant and her MFD Textures are inside the folder)

I tend to keep all textures inside a subfolder for the outfit they are for. So all of my MFD textures are inside my MFD folder inside my Pose folder. This makes finding my textures very easy because everything for that dress that I have installed is located in one spot and because I use subfolders to separate each of the textures I can still tell who created them.

Once you have finished setting up your subfolders you could have something like the following:

Poser6/runtime/libraries/poses/V3 Clothing/Morphing Fantasy Dress
Poser6/runtime/libraries/poses/V3 Clothing/subfolder
Poser6/runtime/libraries/poses/V3 Clothing/subfolder

Poser6/runtime/libraries/poses/M3 Clothing/subfolder
Poser6/runtime/libraries/poses/Aiko/subfolder to break content into clothing, shoes, poses etc
Poser6/runtime/libraries/poses/poses/subfolder to break them into theme or by figure
Poser6/runtime/libraries/poses/plants/subfolder
Poser6/runtime/libraries/poses/props/subfolder to break up by theme or item
Poser6/runtime/libraries/poses/weapons

etc. etc. etc.

Do the same inside any of the library folders with the exception of the morph folders.

I used to do this before I got the hang of multiple runtimes and I liked it well enough but it wasn't as organized as I like, plus one large runtime is hard to backup not to mention that it takes Poser longer to open if you have a huge runtime connected to it.

"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