I sent in an amendment to the IRS, adding $1000 to my income due to a very late 1099-MISC. The IRS paid me my refund again. What to I do?

Did you get 2 refunds?  Or did the IRS just pay you the original refund?  You will still get the first refund.  The amended return is only for the different you get back or owe.  You should not amend until the first return has fully processed and you get the first refund or your tax due payment has cleared.  

Go by the actual 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.

when you amended did it show the refund on line17 of 1040_X. if you added income without withholding there likely would be a balance due as shown on line 20 which you need to pay or wait for the IRS bill that will include penalties and interest.