Hi,
The .encfs6.xml file is always stored in the BoxCryptor Folder - it contains the actual encryption key which itself is encrypted with your password. "Store/Remember Password" additionally stores your password on the local device so that you do not have to enter it every time you use BoxCryptor.
Please see this thread for more information:
https://forums.boxcryptor.com/topic/boxcryptor-storing-the-passwords
Best regards,
Robert