I have two runtimes on my system.  Though I split them one folder up at the My Library level.  I split it there because Daz Studio 4.5 has alot of things stored at that level, and some may reference to specific folders.  I'm not sure about that last part, though.

Some people keep numerous runtimes (or libraries), sorting them based along different preferences..  I keep one with everything I use consistantly, such as Genesis,  etc.  The other is for items that i grab for a specific scene, but won't use again.  I have a friend who splits along theme, with one for key items such as M4/V4, one for fantasy, one for sci-fi, etc.

I would recommend against having a seperate runtime for each 'type' of item though, since these are seperate one level down for Poser

The key is to let Daz Studio know where the different content is.  Use the Content Directory Manager.  There are a lot of ways to get there, but the easiest to describe is:

Main Menu -> Preferences -> Content Library tab -> Content Directory Manager...

Under current sets, make sure to include paths to your the folder your Runtime folder sits in, not the Runtime folder itself.  Do this for Daz Content and Poser Content.  For example mine are:

C:UsersPublicDocumentsDAZ 3DStudioMy Library

C:ProgramDataDAZ 3DMy DAZ Library

C:UsersDSDDocumentsDAZ 3DStudioTemp Library

You might have others for some plugins such as Reality already installed.

You might find more here http://wiki.daz3d.com/doku.php/artzone/pub/software/dazcontent