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My development folder on my local drive is structured to support a design that incorporates 8 unique galleries. The top folder is called alljoyjewelry. Underneath it were folders called sitesupportimages, earrings, keyfobs, hearts, pendants, etc. Each of those folders contained images specific to the gallery. When I was backing up alljoyjewelry I noticed another folder underneath it with the same name, but containing all the images from the other folders. I would like to keep the images in their unique directories. Is there a way to do this? I can’t seem to locate a setting to change that behavior? It will be much easier to maintain and keep current galleries that will be frequently changing in content. Thank you in advance for your help.

By default, all images will be copied to the 'project' folder to keep them all together. Because normally users are not as organized as you are, so images would be all over the place.
But you can control this behavior in Tools -> Options -> Files and Folders -> Asset management. This functionality is also documented in the help.