Unfortunately you can't. Cryptee Docs doesn't support nested folder structures. This has multiple reasons, but there is one main root cause why we chose not to support this.
In order to provide you an unmatched privacy, Cryptee encrypts file & folder names as well as their contents. This means that every folder needs to have a separate encrypted list of names of files within it. Having nested folders complicates the process of encrypting / decrypting file & folder names immensely.
To be specific, we have tested this feature, and found that allowing nested folders occasionally caused real-time-sync'ing errors with file & folder names.
This is a very easy task for unencrypted services, as the server can see the folders, files within, their names and contents, and simply check for what changed, what moved where etc. and simply push only the changes to other devices.
Whereas with Cryptee, since everything is encrypted on your device, and servers can't see/know anything about your folders/files, the process of sync'ing needs to happen on your individual devices.
Meaning that if there were nested folders, every time you moved, deleted or renamed a file/folder, Cryptee would need to download the entire encrypted list of all folders and files, decrypt on your device, update the changes, re-encrypt and upload again. With larger accounts, this of course would cause a significant and unacceptable lag & delay. Therefore we made the decision to not support nested folders.