How do I file a 1040x amended tax return when IRS sent a letter saying I made an error on my original return and we are already paying off the "error" amount?

[matthewmwalk]

For tax year 2014, we submitted our tax return through TurboTax in early 2015.  

We received our refunds (Federal/State) a few weeks later. 

In the summer of 2015, we received a letter from the IRS saying we hadn't paid enough taxes and that we still owed $2,000.  I should have researched it some more since I wasn't sure what mistake I had made, but I ended up setting up a $50/month payment plan.

Just a few days ago, I realized I neglected to include medical related tax deductions in our 2014 return. 

We'd like to file a 1040x to recoup the additional refund we believe we're due, but we're not sure how to fill out the forms taking into account the $2,000 amount the IRS thinks we still owe them.  The 1040x lets you fill in the "original" numbers you filed along with your amended numbers.  How should we include the $2,000 amount in those figures?  I'm guessing we'll need to include a note about it as well, explaining all about it.

[SusanH]

When you do your amendment, you can include the details in the description of why you're filing an amendment; attaching a cover letter when you mail it in would also be a good idea.

Here's how to get started on your amendment:

How to amend a return you already filed