I prepared my tax return using Turbo Tax desktop. Then I manually printed and mailed out Form 4868. How do I file the tax return after I submitted the extension form?
Do I send in by mail or do I have to submit using Turbo Tax?
You don't "have" to do anything.
IRS recommends e-File.
This is independent of what you did with Form 4868.
If you made a payment with Form 4868, you have to enter that on your tax return when using TurboTax.
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