I had six pay periods with no new York states taxes taken out, it amounted t about $3,500. I am estimating that I will make $95,000 by the end of year.

How will that extra money not being taken out affect my state taxes?  Will I have to pay that $3,500 back in it entirety or will it just be factored into my overall taxable income leaving it up to whatever tax bracket I fall into to decide if I owe or get a refund?