If you use TBB to visit a public website that also runs a hidden service for end-to-end encryption(DuckDuckGo for example), will TBB automatically use the hidden service or do users need to manually enter it's onion address?
It must be done manually. There is no interaction between the Domain Name System (DNS) and Tor hidden service hostnames. See this answer about resolution of .onion domains.
Here is a list of custom HTTPS Everywhere rules which when installed would redirect you to the hidden service automatically where available.