thank you for getting in touch with us. When BoxCryptor is installed you'll be asked to create a folder where the encrypted files should be saved. A virtual drive will be created which takes care of the encryption. Everything you safe to this drive will be encrypted.
When you purchase the unlimited version you'll be able to activate the filename encryption. When you're already using the free version, the best way to do this, is to create a second drive/folder combination with filename encryption activated. Then copy the files of your current drive to the new one and you're ready to go. After finishing the process, you can delete the old folder.