Yes, the IRS will review the amended return Form 1040X and reconcile the changes to the originally filed tax return. Since you have already made a payment to the IRS, they will apply your new payment to your account accordingly. If there are any differences you will be notified by letter.
In Part III of Form 1040-X, you'll need to provide a clear explanation of your reasons for filing an amended return.
If amending your tax return results in a higher tax bill, you will need to make an additional tax payment. You can mail a check with the amendment or go online and make a payment at the IRS website after logging into their system. By making a payment now instead of waiting for the IRS to send an invoice, you can minimize the interest and penalties you'll owe.
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