What if i have a balance due after amending my return? I am still getting a refund, but now less. ie refund was $1,000, but now i owe $100, so refund is now only $900.

[DawnC0 · Accepted solution]

The IRS will probably issue you the full refund.  Wait until your original return is processed, then send a check for the amount due back with the amendment (1040X).  You have until the tax deadline to remit the payment, but 3 years to file the amendment.  The IRS does not know about your amendment yet, so they will most likely send the full amount.  

Amendments can't be e-filed.

[VolvoGirl]

You will still get the first refund or need to pay the original tax due.  Then the amended return is only for the difference you get back or owe.  In fact you should not even amend until the first return has fully processed and you get the first refund or your tax due payment has cleared.  And make sure the original refund or tax paid shows up on the amended return.  You can confirm this by printing your amendment and looking at the 1040X. Line 18 should be your original refund amount and line 22 should be your additional refund.  If you paid on your original return it will be on line 16.  If there is an amount owed with the amendment, it will be on line 20.