Haven't tried this, but you probably can already achieve that with the present version.
Create one BoxCryptor folder/drive containing one subfolder per cloud account.
In each monitored folder coupled to a cloud account (e.g your DropBox folder)
you create a symbolic link to the corresponding subfolder in your
BoxCryptor _folder_ (so, not to the subfolder in the BoxCryptor _drive_).
This should make the relevant subfolder appear as a subfolder of the monitored folder
in its (BoxCryptor) encrypted form.
Google Drive apparently does not (or at least: did not) support symbolic links.
The same might apply to some other clousd services.
In such cases you might need to revert to hard links instead of symbolic links.
See https://plus.google.com/+DerekRoss/posts/JDRNpFLYXTe#+DerekRoss/posts/JDRNpFLYXTe
Symbolic links should work across networks; hard links only between fixed drives in one and the same computer.
Obviously, finding the right target for the link is easier if you do not use file-name encryption.
If you want to use file-name encryption, you need to create the subfolders in the BoxCrytor _drive_,
which will result in an encrypted name for that subfolder in your BoxCryptor _folder_,
and then create your link to the encrypted subfolder name in the BoxCryptor _folder_.
