How do I correct disorganized files?

I have developed an unknown problem with my files when viewed by file location. I do not know what caused this problem, but it is a real problem. When I look at my files in the "Folder Location" view, there are these levels of folders: Pictures/Adobe/Other Photos/Photoshop.com/multiple individual folders. Then branching out from "Other Photos is a second "Photoshop.com" folder that is grey in color with a second complete set of my individual photo folders that are also grey rather than manilla in color. This doesn't seem to be right, nor an efficient, simple organization of my individual folders. How can I fix this and end up with a simple filing system?

Grey folders in Folder Location view normally indicate that you've used another program, such as Windows Explorer, to delete folders containing photos that are in your catalog. 
You're indicating something else, that there are two folders shown in Folder Location view with identical paths:
Pictures\Adobe\Other Photos\Photoshop.com\
If that's true, then that suggests a bug in PSE. 
Do File > Reconnect > All Missing.  Are any photos indicated as missing? 
Those folder names indicate that at some point all those photos were downloaded from your Photoshop.com account.  Sometime in the past, did you upload or sync your photos to Photoshop.com and then create a new catalog, perhaps on a new computer?   I'm asking, because if something goes wrong with the sync with Photoshop.com, you could end up with duplicates of your photos.

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