1. Yes, ignore state wages on w2. You can fill in the amount that is correct from your own math or use the program and the full amount to apportion.
For example: If you worked 5 days in MA out of 260 total working days, that is 1.9% of the income earned while in MA. If you earned $100,000 and 1.9% was in MA, you could enter $1,900 for state wages on the w2 - or the full amount and apportion in MA program.
2. You don't want to pay MA every paycheck when you are barely there. You could make estimated payments. See Massachusetts DOR Estimated Tax Payments - Mass.gov
3. Your residency is NH so that is where you want taxes to go.
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