If you disagree with an IRS notice, generally the best response (rather than doing an amended return) is to submit the response form with a signed statement explaining why you disagree, along with any supporting documentation you might have. Be sure to keep a copy of the correspondence. Include a phone number at which they can contact you, and make sure your last name & SSN & the tax year are on each page of your response. Personally, I wouldn't enclose a check until the IRS formally accepts or rejects your disagreement.
**Answers are correct to the best of my ability but do not constitute tax or legal advice.
