If IRS sent you a letter requesting the forms 8962 & 1095-A, and you input the 1095-A and are now seeing an amount owed on an amended return (1040X), you do not need to send IRS the 1040X. If you look in their letter, they have probably instructed that you don't need to amend, but simply to send/fax the two forms requested. That's all you have to do.
Regarding the amount owed, take a look at the 8962, line 29. That's where you should see the figure. It's a repayment of the Premium Tax Credit you received as a subsidy to help with the insurance premiums.
The PTC can be given in advance as a subsidy, and its based on your estimated income, which you included with the application when you signed up at the beginning of the year. Now, after the year ends and your actual income is known, the PTC is "reconciled" on the 8962. So if your estimate was too low, you pay some of the subsidy back. If it was too high, then you receive additional credit on the tax return.
