Broke Backup File Structure

I have just come to realize how the WD smartware structures the data, though a little to late, partly due to my own ignorance I admit.

I have a 1TB my book and its half full, why? because the thing makes 5 copies of A LOT of garbage.  Yes, I now realize that the number of copies can be changed, and perhaps I could have elected not to back up the garbage files, but still dont know how.

Because I was unfamilair with the way this system works, I went ahead and unintentionally broke the file structure on the drive, meaning I started moving files around on my own, and got rid of the WD SmartWare.swstor dir, and all the other stuff that looked “strange”.  Now I realize the the “smart ware”  will not see the volume I was once backing up to, therefore I am in a pretty bad situation.

I believe the files are still there because my drive is still half full, and I didnt delete too many things, just rearranged. 

Are there any recommendations or utilities I can use to get Smartware working again, or somehow methodically fish through 500G of usesless configuration settings so I can get my real files and start trying to regain control here?   

Thank you in advance. 

You’ll have to format the drive to clean it and then start over.