I'm not specifically familiar with MA tax rules and TT software. But, the way it works in all states is that you allocate your income as MA or not MA income in the state interview.
One (usually) helpful technique is to show NH on lines 15-20 at the W-2 screen in the federal section of TT. Since NH is a no income tax state, your actual W-2 is probably blank in boxes 15-20. When you enter your W-2, in TT, enter NH in box 15 and the box 1 amount in box 16.
