Why did you get the 1099R? If it’s not taxable and doesn’t affect your return you don’t need to amend. What code is in box 7? Amending won’t affect your first refund. In fact you need to wait to amend until the first return is done processing and you get the first refund. And the amended 1040X return won’t be ready until until Feb 15.
Then the amended return is only for the difference you get back or owe. I think the cover sheet shows what the original return WOULD have been if you did it right the first time.
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.
