So entities extracted by duckling shouldn’t be labeled in your training data. I think we fixed that in interactive learning either in 0.15.0 or in the latest master. We would advise you rely on duckling to extract time, becasue it’s a lot more robust than trying to get the crf to extract them. You can post process these entities in a custom action if needed.
And yes, you should list any entities you want duckling to extract in your domain file. You can also restrict the ones that should be extracted in the dimensions section in your nlu config file