I don't like built-in encryption features in file transfer or backup apps too much, because they are often proprietary and that may make it hard to switch to another client.
As a workflow example, I personally encrypt my archives with gnupg and store them on external hard drives and additionally upload them to Glacier for disaster recovery.
On the other hand I find manual local encryption a bit cumbersome workflow wise...
> Amazon Glacier handles key management and key protection for you. Amazon Glacier uses one of the strongest block ciphers available, 256-bit Advanced Encryption Standard (AES-256). 256-bit is the largest key size defined for AES. Customers wishing to manage their own keys can encrypt data prior to uploading it.