Agree with Gillieworm - start taking her out for the toilet - they are very clean creatures............ During the night we used to take Rocky out every 2 hrs for the first week and then every 3 hrs, some puppies need to go out more often.
But the results where quick as within about 3-4 weeks he was sleeping through the night from 9 pm - 6 am!!

Also if he is toileted regularly during the night and he is sleeping in your room then he should stop the barking/howling during the night.

PS Can he see out of the carboard box?

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Proud owner of Rocky the Yorkie, born July 2008, who came to live with us at 8 weeks old