It is almost impossible to try and keep track of some many runtime folders without a structured, logical arrangement that works for you.  I tend to create runtimes for projects and load content specifically used for that project.  Once done, the runtime folder is either transferred to disk and deleted off the HD or completely deleted if certain I will never go back to it.  The most used content get their own runtime folders for easy access (i.e., Poses, Props, individual characters, Themed, etc.)