Let's say I fix your computer and send you a bill for $300. Then you pay that bill. The bill I sent you will not "magically" update itself to say you paid it.
Likewise when you complete your tax return and it shows you owe the IRS $300, when you pay that $300 to the IRS your tax return is not going to magically update itself either. Turbotax has no way of knowing that you actually paid what you owe. Your return will show that you owe that $300 forever.
If you're concerned about it, then simply attach your receipt of payment to your paper copy of the tax return, and file it away.
