Did you file yet ? If you haven't filed......
To enter or change the amount you paid with an extension (including state extension) go to
Federal Taxes (or Personal for desktop H&B version)
Deductions and Credits
Then scroll way down to Estimates and Other Taxes Paid
Other Income Taxes - Click the Start or Update button
Next page second section Payments with Extension
To enter, change or delete a payment made with an extension request (Federal, State, Local) -
Click on Federal Taxes (Personal using Home and Business)
Click on Deductions and Credits
Click on I'll choose what I work on (if shown)
Scroll down to Estimates and Other Taxes Paid
On Income Taxes Paid, click on the start or update button
On the next screen select the type of extension payment made and click on the start or update button
Or enter federal extension payment in the Search box located in the upper right of the program screen. Click on Jump to federal extension payment
The federal extension payment will be shown on Schedule 3 Line 10. The amount from Schedule 3 Part II Line 15 flows to Form 1040 Line 31
If you did already file with the incorrect amount, wait until the IRS finishes processing your tax return and you get the refund (if any). The IRS might correct the payment amount for you, since they know how much you paid. If they don't correct it, you will have to file an amended return to make the correction.
You need to report all your income on your tax return.
If you received another W-2 after filing, wait until the IRS either reject or accept your return.