How the IRS handle amended returns when you've already paid them?

For last year's tax return, I had to pay the IRS. However, I noticed this year that I did not file as "head of household" when I was eligible for it. I just amended my return. My return shows that I still owe money but less. Do I mail this amended return that shows I owe money even though I've already paid the IRS? Will the IRS pay me back the difference based upon this amended return?