Get your taxes done using TurboTax

So, if I made those payments this year to be applied to 2018 and then submit my tax return without reflecting those payments, does that mean I have to pay the amount again, knowing that I don't owe as much as the return shows?   Do I file for an extension, pay the actual net tax liability with the extension, and then file the actual return when the IRS shows that all taxes due have been paid?