I filed and extension. Does the IRS take out the money later since I gave them my routing and checking number on the TurboTax form? So far nothing has been taken out.

Yes, they will need time to process your extension before they take the funds.

Thanks. I don't want to get penalized. I almost made a payment last night via another route but I don't want to double pay. How long does it usually take to process and take the funds? A day or two? Thanks in advance!