Do I understand this correctly: after installing Boxcryptor and adding e.g. iCloud Drive as Cloud provider, I can see everything that's already on my iCloud Drive inside the Boxcryptor Disk view, exactly as if I opened iCloud Drive directly in Finder; the only visual difference are encrypted files or folders, which are displayed unencrypted in Boxcryptor, and encrypted / unreadable in Finder.
To add files or folders without encryption, I need to make sure I'm using iCloud Disk in Finder.
To add files or folders with encryption, I either have to use iCloud Disk in Boxcryptor (which looks 99% identical to Finder), or use Finder and then switch to Boxcryptor to find the file/folder and then encrypt it.
I guess what I'm missing is a (switchable) view in Boxcryptor where I only see encrypted files/folders, as this might make it more easily viewable which view I'm in, and therefore what's going to happen to the files/folders I'm about to put in there.
Also, I'm positive that the warning message when deleting a Cloud provider in Boxcryptor could be improved – «all your files in iCloud Drive will be removed» is definitely not something I, and I guess most Mac users, would like to happen.