Before deleting the folders, I'd make sure there is nothing of importance to them.
The guide I posted much early describes how to move the "DE" folder structure to the StableBit DrivePool Structure, as well. Moving all of that data into the pool.
Here is that link again. http://wiki.covecube...vePool_Q5463715
Once the data is moved out, then yes, delete the DE folders, but don't do so beforehand, unless you don't care about that data.
As for the Client Backup Database, you can absolutely move that onto the pool. And we highly recommend enabling duplication on that folder, because it can be very bad if you lose even one file of the backup database.
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Lots of "Other" data on your pool? Read about what it is here.