“However, I am assuming there is some penalty, that will be significantly more than the unpaid tax and interest on the unpaid tax.”-->No, I don’t think so. If you owe taxes, the IRS will calculate penalties and interest on the amount owed. There are three separate penalties:Failure to File Penalty;Failure to Pay Penalty’ Interest. The failure-to-file penalty is calculated based on the time from the deadline of your tax return (including extensions) to the date you actually filed your tax return. The penalty is 5% for each month the tax return is late, up to a total maximum penalty of 25%, but you are not subject to FTF penalty as long as you file your extended return. As you can see, you must file Form 4868, Application for Automatic Extension of Time To File U.S. Individual Income Tax Return by the due date for filing your calendar year return (usually April 15) or fiscal year return. The failure-to-pay penalty is calculated based on the amount of tax you owe. The penalty is 0.5% for each month the tax is not paid in full, so the penalty( assume that you are one month late on paying your tax) for you ‘d be $16*0.005=$0.08 per month;there is no maximum limit to the failure-to-pay penalty. Interest is calculated based on how much tax you owe. Interest rates change every three months. Currently, the IRS interest rate for underpayment of tax is 4% per year, so your interest ‘d be $16*0.04=.64/12*1=$0.053, so your total penalties and interest‘d be less than $1.00~$1.40 for the first month.
“Can I just send in payment voucher with a check for $3 prior to April 15, and no accompanying amended tax form, and let the IRS keep the change?”-->In general what your CPA said is correct as he is the person that prepared your return; however, in general,NEEDLESS TO SAY, you always need to report the correct amount of income. You can also report any deductions you forgot or recalculate your tax credits based on the new income figures.