For my first time filing taxes, I used TurboTax online (around 11p.m. April 14th, big mistake) and got an extension because I lost my W-2. I chose to mail in my estimated payment, but didn't realize they took the postmark on the check, and not the time I filed to consider me late. Because TurboTax doesn't let you change your payment options, I used one of the IRS's recommended processors to avoid late fees. I just finished my return, and TurboTax had no option to indicate that I had already paid, so I paid there too, just to be safe. Will the fact that I submitted two payments from different sources affect my return? And how do I get back all the extra money I paid? I ended up using Pay1040 for my estimated extension payment, and paid through TurboTax for my actual amount due.