Hi Alessio,
Thank you for your suggestion. This is currently not possible but I will add it to our internal list of feature requests. What you can do, is to create a folder "Internal" which is encrypted. Every file you store in this folder will automatically be encrypted.
We do not have command line arguments (or similar) to encrypt/decrypt a file. Files are encrypted by storing them in an encrypted folder in the Boxcryptor Drive.
Best regards,
Robert