Yes, the things are designed to merge - unless you want to split content you should unpack all parts to the same folder so that the Runtimes are meged together (and with any other content already installed) and that Runtime should be in a folder you have selected as a Poser content directory (not in a sub-folder).

Poser files contain relative paths - Runtime and any sub-folders. What you are doing when you set up content directories is giving DS a list of places to look for the Runtime folder.