Crate and Independence training

I have a 12 week old labradoodle pup. when we got him we immediately put him in a large training crate and drove 3 hours back home. He was whimpering and howling and vomited from Carsickness it was his first ever experience on a car . he was raised by the Amish. Currently we are trying to train him to be home alone and crate train to as well. We carry him into the crate everytime then he begin to whimper once the crate doors Close after a couple minutes he settle down and lays down until another disruptive occurs like someone new coming into the room. We are hoping that he will learn slowly that the crate is his home and that it is fine to not be with humans all the time. Do you think this method is okay for the puppy? Do you think he will develop seperation anxiety or cure the puppy anxiety he has. Thanks!!
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