I have the messiest content folder. Folder are shown that are empty and or duplicate. It's hard to find what I'm looking for. Needs tips on cleaning up this mess. You can see the problem in the  image. It what be great if all figure went into one figure folder, all mats went into a folder, etc.

You can remove empty folder via Edit>Preferences>Directories tab, click the button at the top and select Poser content directories (since that's what those appear to be).

To add a new content folder, for Poser files, you need to create the folder you want to use and point the installers for the content to it, or unzip the content into it (you want the Runtime folder to end up in your chosen folder, where it will slot its files in around those that are already there.

You can move files around within and (as long as you use only D|S and not Poser) between libraries (that is, the Camera, character, face, hair, hand, light, pose and props folders in Runtimelibraries) and between Poser content folders.