Let's say that an individual filed his Federal 1040A and expects a decent refund. Let's say that this individual made a serious mistake in said tax return and only caught it after said filing was complete. Let's say that this mistake means that the individual would still get a refund, just smaller than originally projected. How does one follow up on this? Does one file a corrected / amended return IMMEDIATELY? Or does one wait until the return is processed and the original refund delivered, THEN file the amended / corrected return and mail in the appropriate payment? My concern for this hypothetical individual is that if one files said amended / corrected return too soon, the IRS will have a lot of room to create embarrassing blunders that make everything much too complicated. What say the resident experts?
How big is the difference? If I remember correctly, owing less than $1,000 on your taxes doesn't lead to any late penalties, but if you owe more than $1,000 they can start to add up. So in that case, waiting to file an amended return could come back to bite you. I assume that, even if the mail ends up opened in the wrong order or whatever, a 1040-X will automatically supersede a 1040 even if the 1040 is processed later.
I, personally, would call the IRS, knowing I'll be on hold for several hours, and ask the IRS directly. Done it before. Will probably do it again.
I'd file an amended return to avoid name calling. If you get the full refund, don't spend it. Send it to me for safe keeping.
I've done similar things as you describe. The IRS advises you not send in an amendment while they are still processing your original submission. It can actually delay getting the proper refund amount. Quite often (if you aren't itemizing and you just have a very simple tax situation) the IRS will catch your mistake anyway and send you the documentation explaining why your refund amount is different than what you thought.
I have called the IRS too. Sometimes it takes a while, sometimes you get through quickly. But every time they helped me out a great deal.
The tax prep industry lobby and the anti-tax lobby are both equally committed to making the filing process as painful as possible.