Original Return showed owing money but amended shows refund - and IRS processed Original and withdrew money

[CLS18]

HI, 

I have my taxes prepared every by CPA due to also having an LLC. There was a mistake made to my tax basis this year which was caught AFTER my CPA filed my initial tax Return. My initial tax return showed that I owed both State and Federal Taxes. Once I followed up with a few questions, my CPA realized there was a mistake made and the refiled an Amended tax return, which then showed that I would receive a refund for both State and Federal. She Refiled with days of the initial tax filing. As of today, I had two deductions from my checking from both State and Federal leading me to conclude that my initial has been fully processed. Now, I am concerned that my Amended Return will 1) Not process correclty. 2) Only reflect the initial refund amounts 3) How to even begin the process fo disputing the two drafts with both my state and the federal government, and can I dispute? 4) Will the Refund from the amended return reflect the calculation error and Ill recieve a refund for the deductions in addition to my actual refunds.  I am pretty annoyed that my CPA put me in this position and also didn't explain that this would even be a possibility. Could someone please shed some light. I have tried to research the context around this particular situation, and haven't been able to locate a clear answer. 

[rjs]

You should discuss your concerns with your CPA, and let her explain it to you.

It's normal to pay what you owe on the original return, and then make any adjustments on the amended return. The original return is always processed as if the amended return does not exist. The amended return is processed later. That's the way the system works. The IRS and the state do not take the amended return into consideration when processing the original return, even if they have already received the amended return.

The refund on the amended return represents the difference between what you owed on the original return and the amount that you would have owed if the original return had been correct. The amended return is an adjustment to the original return. It's not a replacement for the original return. On your federal Form 1040-X the amount that you paid with the original return should be included on line 16. The state amended return would have a similar entry.