Not following. What does any of this have to do with Extension payment? You should have waited to amend until the original return was done processing. Where do you expect to see the 1,000 as taxes paid or add to your payments? So your original return refund would have been 4,000. You owed 1,000 back. I think you still can apply 5,000 to next year's tax return. Although I don't know how amended returns work when you applied some refund to next year.
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.
Ignore any 1040V voucher that prints out and the new 1040. Those are what your return would have been if you had not needed to amend.
