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.
