I know that I can create a subdirectory, encrypt it, and then all the files I add to it will be encrypted.
What about files added at the top level?
I guess I could put everything in a subdirectory. I feel like I must be missing something.
with "top level?" you mean the root folder on the Boxcryptor drive?
Well, that's not possible.
The root folder is reserved for locations.
By adding a file to a folder (which is unencrypted) will trigger a warning if you want to encrypt.
By adding a file to an already encrypted folder will just encrypt the file automagically.