If a man gives his wife a get through a shliach...only because they do not wish to see each other....at the time of the writing of the get is it okay for the woman to be in the same neighborhood or does she have to go to another boro, like if the get is being written in brooklyn should she go to Manhattan for the duration of the writing?

We can learn from cases in the Rabbinical Court in Israel that the wife can be physically present in the same neighborhood. However, it can happen that a private Rabbinical Court in the US may require the wife not be in the same area so to "justify" the administering of the get through a proxy--shaliach. If the Rabbinical Court does require it, it would be best to comply with their wishes so that everyone is of the opinion that the get is 100% kosher--this actually is a means of protecting the woman so that no one can come later on and question the validity of the get.