Do we have to send a check to the IRS after filing a 1040X knowing we're getting a refund?

I sincerely hope you have not mailed that amended return yet. If you have, you very well may have created a headache for yourself (more like a migraine).

You should not amend your return until your already filed and accepted return is completely processed. Please read all of the below to see where I'm coming from. (My impression is that you have not mailed your return yet. I hope I'm right)

Already E-Filed and Need To Change

If you have already E-filed your tax return and need to make a change for any reason, then you have no choice but to wait until the IRS processes your E-filed return. If the IRS rejects your E-filed return, then you can just make the necessary changes and resubmit it.

If the IRS accepts your E-filed return, then you must WAIT until the IRS has processed your return. If you have a refund due your return is not processed until you have received your refund. If you owe taxes, your refund is not processed until you have paid those taxes and your payment has cleared your financial institution. Once processing is complete, you will need to file an amended return. You can not e-file an amended return. The IRS says you can’t. You have to print it, sign it (both the 1040 and 1040X) and physically mail it to the IRS.

If your E-Filed return is pending, and you change anything on your copy of your return, then you are guaranteed to have major issues with correcting or amending it later. So for your own sanity, do not touch anything until it’s time, as clarified above.

An amended return must be printed, signed and mailed. The IRS says so.

If my return is accepted, why do I have to wait for my refund before I can amend it?

Just because the IRS has accepted your return, does not mean that they agree with it. Sometimes, the IRS will “catch” your error (or some other error you don’t know about) and go ahead and correct it for you. You’ll know that when your refund is not what you expected.  So you have to wait for the refund.  If that happens to you, then you will receive a letter 3-4 weeks after you receive your refund, explaining what was changed, why it was changed, and with instructions on what actions to take if your dispute the change. If you receive such a letter, post in this forum with the details (without including personal information) and we'll try to help you get your copy of the return in agreement with the IRS changes, so you won't have issues importing next year.