Hi jgarner,
To encrypt a folder with boxcryptor, simply right-click the folder within the Boxcryptor drive and select Boxcryptor -> encrypt.
Alternatively, you can simply drag and drop a folder from somewhere else to the Boxcryptor drive, Depending on where you drop it you might get asked if you want to encrypt this folder, or the folder will be encrypted automatically. For more information on how boxcryptor works please have a look at: https://www.boxcryptor.com/en/boxcryptor
Kind regards,
Florian