Answer 1: The Download Folder in Poser is an extra folder which contains its own runtime.  I'm surprized that your content runtime did not replace the original.  However, that will not present any problems.  It will show up in the library as an empty folder.

Anwser 2: Yes, you can tell PoserPro 2010 where your runtime is located, either on a local HD or external.

Answer 3: Each of those folders you noticed in the post image has its own runtime folder within.  Basically, the library hierarchy is duplicated for each folder.

Answer 4: On PC's, directing the OS to replace a folder only adds content to the folder unless it finds a duplicate file within (i.e., readme's, license txt, etc).  Earlier MAC versions completely deleted the original file and replaced it with the new.  I don't know if that has changed.  Keep in mind, the authors create unique content folders within the runtimes to identify their products.  Notice in my image under Victoria 4>Runtime>libraries> Character, there are 2 vendor folders.  The other category folders may contain more or less content depending on the type.