this is expected behavior. Boxcryptor uses a virtual drive to intercept all read and write operations and encrypt and decrypt your data on the fly. That is why you see the folder 2 times.
One is a virtual drive which mirrors the content of your locations and one is the real directory where the encrypted data is stored.
When you put a file into the virtual directory Boxcryptor encrypts it before it is written to your disk to prevent your cloud providers sync client from uploading any data before it is encrypted.
When you open a file in the virtual drive Boxcryptor reads the encrypted file, decrypts it on the fly and passes the data on to the application that opened it. This way the physical copy stays encrypted but your applications can access the files as usual.
Accessing the data directly in the real folder circumvents this system.
For more details please see https://www.boxcryptor.com/help/work-with-files/
Please make sure to always use the virtual drive.