For example If I reside outside New York City, will I pay at both place?
No. If you reside outside New York City and you are exempt from the vehicle use tax in the county where you reside or have a business
What are New York City places
New York City Bronx, Kings (Brooklyn), New York (Manhattan), Queens, Richmond (Staten Island) Vehicle use tax - $ 30 for two years $ 15 per year. And Supplemental MCTD fee - $ 50 for two years $ 25 per year