Here's the bottom line.
If your originally filed return showed that you owed the IRS, that payment was due by Apr 18, 2017. Period. End of story. If you did not pay it, then it is still due. The amended return does not figure into this at this point. Since you have already received two letters, if you do not pay the amount due ASAP, there will be no third letter. instead the IRS will start placing liens on any real property you own, usually starting with your primary residence.
Amended returns are processed by hand since you have to mail them in and they can not be e-filed. It can take 8-16 weeks or longer to process the amended return, depending on it's complexity.
So I would highly suggest you go to http://www.irs.gov/directpay and pay NOW. You can deal with the aftermath later. Which aftermath you deal with is up to you; the IRS owing you a refund, or the IRS taking your house.
Yes, I agree it's not right. But that's the way it is. We have to play by their rules, or you *will* lose.