Poser will only look at the Runtime directly below it. It will ignore your deeper folder. I would copy the second Runtime into your Poser root. You will recieve errors about directories already exists: click yes or yes to all. IF you have different items in the second Runtime they will be added to your working folders. Then you can delete the second Runtime folder.
MAKE A BACKUP OF THE POSER DIRECTORY BEFORE YOU DO THIS!
I've done the many times myself. Usually its my fault because I've chosen one level down too many on a prop or figure install.

Good luck.
Thorn