If you aren't able to use the feature within TurboTax, you can just select the pay by check option within TurboTax and then schedule a Direct Debit instead on the IRS website (use link below). No, you don't indicate that you filed an extension anywhere when you file your return. And, yes, any interest owed would be billed afterwards.
<a rel="nofollow" target="_blank" href="
https://www.irs.gov/payments">https://www.irs.gov/payments</a>
