"From the link you sent, I meet several of the conditions to be considered a bonafide office"
Add them up and see if you meet one of the requirements.
"In order for an office to be considered a bona fide employer office, the office must meet either:
a) the primary factor, or
b) at least 4 of the secondary factors and 3 of the other factors"
Q. Do I need to fill out my W4 for NY in a particular way?
A. No. There i nothing on the NY IT-2104 to cover your situation
Q. Do I need to pay the taxes through out the year and then complete my taxes in a particular way to receive that paid money back?
A. Yes. You file a non-resident return and allocate your income as NY source or not NY source.
