If your request for extension was accepted by the IRS then now all you do is file normally. The IRS knows you have an extension. You can e-file the return. If you run into any trouble with e-filing, try using zero as your AGI. If you have problems with e-filing that you just cannot overcome, then you can print, sign and mail your return. If you file by mail you should expect it to take about nine months to be processed.
When you requested your extension you were supposed to pay your estimated tax due. Did you enter the payment you made into your tax return? Go to Federal>Deductions and Credits>Estimates and Other Taxes Paid>Other Income Taxes