Ahh see what you mean
BoxCryptor creates its own drive, where you can read all the files in English
However you can read the encrypted filenames etc wherever you decide to store that info
Example being boxcryptor "in english" is drive W
however actually stored in f:\gdrive\boxcryptor (encrypted)
G drive is wherever you locate the folder. I do not use DropBox (I use box.net as I got 50gb free).
So for me...
I'll use boxcryptor - encrypt all filenames and files and store (where I like)
I'll use Goodsync. - upload to gdrive, Amazon S3 servers, WebDAV, Box.net, skydrive etc. sync multi files/folders, etc to seperate folder paths etc, exclude files, etc...
So I think you can achieve what you are trying to do. I guess it just depends on the limitations of sync (upload) software you are using - some sync software like to create virtual drives and some allow file / folder choice (better for me)
For me BoxCryptor is brilliant as it can decrypt filenames with its mobile app, with google drive now - which is a massive plus. And I can keep everything encrpyted.
Hope it helps