How do I file after an extension? turbo tax is asking for a payment method, but we have already paid. how do I file without repaying?

You file normally.  Nothing special except make sure that any estimated payment you made for your 2018 tax due was entered.

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