Wait to mail or efile the amended return until after the IRS is done with the original return and sends you the refund.
You will still get the first original full refund (and keep it) or need to pay the first tax due. You should not amend or change your return until you get the refund from the original return or your payment has cleared.
The amended return will only be the difference you get back or need to pay. You can confirm this by printing your amendment and looking at the 1040X. Line 18 should be your original refund amount and line 21 should be your additional refund. If you paid on your original return it will be on line 16 (but don't include any penalty on 1040 line 38). If there is an amount owed with the amendment, it will be on line 20.