Unfortunately all encrypted folders reside under the Encryptor folder. You will need to either refactor your storage scheme to use the Encryptor folder as a root or duplicate everything.
Another issue we are running up against is that odrive’s automatic synchronization with encrypted shares is functionally one way only, at least on Windows computers. Changes to a file on one computer are properly synced up to the cloud. If you use odrive on more than one computer, changed files will not sync back from the cloud until either a manual sync is performed or, if you are lucky, you browse to the relevant folder in Explorer. see this thread for full details.