You would be better off creating a new runtime (or several runtimes) to split your content.  I would house related files together for convenience and ease to locate.  Straightforward installs can be moved from runtime to runtime, only file associations related to older .pz2 generated files may have issues later. 

The Collection tab, or Favorites in P8, will only establish links for popular items under one folder.  It will no way transfer files to a new location nor will you lose items when you delete from such folders.  Commonly used content from differerent runtimes will just be conveniently located in one area rather than switching and searching between runtimes.