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.

---

From a post I made some months back on how I use Multiple Runtimes:

http://forum.daz3d.com/viewtopic.php?t=9060

I used to lose things all of the time and became so frustrated that I gave up on Poser a number of times and uninstalled it.

I tried a number of ways to sort my content, and finally settled on Multiple Runtimes.

I currently have about 40 runtime folders and know exactly what I have installed and where to find it.  Examples of some runtimes that I have:

V3 Character addons (includes the install of V3 and her morphs)
V3 Clothing
M3 Character addons
M3 Clothing
Aiko
Plants
Backgrounds/Environments
Angels and Faeries
Mermaids
Christmas
Halloween
Lighting
Poses
Props
Hair
Vehicles
Animals
Miscellaneous (for anything not large enough to warrant having  it's own runtime IE: Millennium Dragon)

A runtime is a runtime is a runtime. They are all set up using the same structure and they all function the same. All an "external" runtime is is a runtime folder that sits outside of your Poser folder. It doesn't need any special consideration and it doesn't need any special set up or any special way of installing the folder. You treat it just like you do your main Poser runtime. 

Another way you can do it is instead of using multiple external runtimes, you can set up separate sub folders inside your main Poser library folders.

For example, inside the library/character folder, you could set up sub folders for:

V3 Clothing
M3 Clothing
Aiko
Plants

*You can further sort them by adding more sub folders to the inside of those, for instance:

Inside the V3 Clothing folder you could create sub folders for each outfit*

In the library/pose folder you could set up sub folders for:

V3 Clothing
M3 Clothing
Aiko
Poses

*You can further sort them by adding more sub folders to the inside of those, for instance:

Inside the V3 Clothing folder you could create sub folders for each outfit: For example:

Morphing Fantasy Dress
Morphing Cocktail Dress
Morphing Starlette Dress
etc
etc
etc

Then when you install a texture for those outfits you put the texture inside the folder for the dress/outfit it belongs to. This way all of your textures for the MFD are inside the folder called "Morphing Fantasy Dress" and way easy to locate :)

*Another thing I do to help me find things is naming continuity.  I discovered quickly that merchants don't always name their folders the same thing from one library folder to the next. That doen't help me to find something when the folder inside the character folder is called "jane's dress", while the folder inside library/poses is called "dress MATS" or "smith_dress".  So I rename ALL of the folders that the item is creating  to something I will recognize when I look at it IE:  "Jane's Bride Gown". That way when I want to use that outfit, I can look through all of the library folders to see if I have other folders called "Jane's Bride Gown" that I know go with that dress.

TIP:  Never install or unzip a package directly into your runtime folder.  Do it to a folder on your desktop. Browse the folder, organize it the way you want, then move the runtime/contents to it's final resting place in your runtime.

"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