The Navy is not paying for his medical school. He has two separate W-2's: the Navy, and the hospital where he is doing his residency. Because his Home of Record with the Navy is Florida, the income he receives from the Navy he owes only Federal and Florida ($0) tax.

"As a nonresident, your military compensation is not subject to New York State income tax. However, other income that you receive from New York State sources may be subject to tax."

That above line from NYS is the challenge. The only way (that I am aware of) in Pro-Series to not subject your income to NYS taxes is to file as a non-resident of NY. However, the income he receives from the hospital has to be treated NYS income (he lived and worked there), as only military compensation gets unique treatment here.

I currently have him setup in ProSeries to file as a part-year resident of NY (apportioning the months he lived there to the income needed to be taxed by NYS) and a part year resident of FL (apportioning the months he lived there to the income needed to be taxed by NYS).