Is all of "vào ngày hôm qua" necessary to say yesterday?
Nope, you can just say "hôm qua" which means "yesterday".
Is there any difference in meaning when you put it at the beginning of the sentence versus the end?
Depends on what you are trying to emphasize. If you want to to emphasize the time, then put itat the end and vice versa. But the difference is not that big don't worry too much about it.