If you pay the tax with your return, it should not affect your 2011 refune because you have no outstanding tax liablity. To be safe, take the 2011 tax return and the check personally to the local office and get a receipt for the payment.
Phillip M. Smith Jr.
Tax and Business Attorney
Phone: 855 IRSTAXBIZ
THESE COMMENTS ARE NOT LEGAL ADVICE. They are provided for informational purposes only. Actual legal advice can only be provided after consultation by an attorney licensed in your jurisdiction. The answer to question does not create an attorney-client relationship or otherwise require further consultation. Mr. Smith is licensed to practice law throughout the state of California with offices in Los Angeles County. He is authorized to handle IRS matters throughout the United States, and is also licensed to practice before the United States Tax Court. His phone number is 323-292-4116 or his email address is email@example.com.