For US taxes, you fill out a form indicating how many exemptions you're claiming and the employer then withholds the state and federal taxes from your paycheck. By April 15 of the next year you have to file a tax return, calculating what you actually owe (it can get complicated with all the deductions) and if you've had too much withheld, you get a refund. If you haven't had enough withheld, you have to pay the difference.
You should be OK. $85,000 is just over $7,000 per month before taxes. This website has a calculator for what the pay would be after taxes. Entering Massachusetts, married, and 3 allowances (for the 3 people) it comes out to about $5,500 a month after taxes. Note that if you're paid every two weeks, you will have less take-home pay most months and twice a year get a third paycheck in a single month, so you'll have to budget.
PaycheckCity.com | Paycheck Calculator
You should be able to get a nice 3-BR in Newton for $2500 or maybe a bit less, though you might have better luck in a 2-family house rather than looking for a single family house. Many of them have nice yards that you can use. Ultimately you'll have to decide if you'd rather have somewhat less expensive housing elsewhere or pay a bit more to be in Newton.
Not sure which end of the South End you'll be working in, but if you find a place near one of the Newtonville, West Newton, or Auburndale commuter rail stations along the Mass Pike on the north side of Newton, it will be quicker than the Green Line. About 20-25 mins to Back Bay station and then you can walk or take the bus from there to your workplace. It may even be under an hour, depending on how far your office and your home are from the train stations.