To be honest I don't understand your question entirely.
As far as I understood you want to have a folder which is entirely encrypted within your Cloud Provider's location.
This is exactly the approach Boxcryptor provides: In your Boxcryptor Drive, open up your provider location and create a new folder anywhere (including sub-folders). Boxcryptor will ask you if that location should be encrypted, select "yes" and all other files dropped into this folder via the Boxcryptor drive will then automatically get encrypted.
For more information, have a look at the video here: