How to file amended return when original return has Irs detected error plus my major error

Irs found a $50 error in the credit I took against my estimated taxes for 2015 and billed me for it. I can't explain it since I use Turbo Tax and none of my copies matches the credit they say I was entitled to but I believe them. Now I found that I also grossly under reported my deductable local taxes and a few hundred dollars of medical expenses. If I were to amend just this part of Schedule a I should get back about $800 in overpaid taxes so it seems worth it. However if I used the Turbo Tax form I have, it still has the incorrect value for the credit against my estimated taxes in it and I would have to override it to file the form electronically (I'm not married to efiling it and I think overrides would block efiling anyway).
Should I file the amended form just the way I filed the original with only my corrections, and include the erroneous credit that the IRS detected, or will that generate yet another flag to them and we will run circles trying to explain that I already paid that last year? Or do I incorporate their notification and my payment into the amended form and mail it to them? With or without explanation?
Thanks, Jo
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On Saturday, March 12, 2016 at 11:36:17 AM UTC-5, jo wrote:

There is no way you can e-file anything other than an original return (or a request for an extension), so you have to respond in writing. The simplest way is to include everything in your response to the bill. Include any changed forms along with an explanation of what the changes are. Since you have the IRS's attention, your response will go directly to an individual who will be able to review everything and contact you if further explanation is needed.
Ira Smilovitz
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