If Form 1040-X is not showing up in forms mode you did not start the amended return correctly. Start over, and follow the instructions at the following link. I think all of your other problems will be resolved when you start the amended return correctly.
How do I amend my federal tax return for a prior year?
I do not recommend applying the refund from the amended return to a future year. It's too likely to lead to errors at the IRS, which would cause more trouble and confusion. If you need to make an estimated tax payment for 2025, make the payment separately and let them send you the full refund from the amended return. You have until April 15 to make a first-quarter estimated tax payment.
