After you file

I'm still not 100% clear on your question. Did you file an original return with a balance due and then amend the return and are now due a refund? Is the money you say you are getting back a portion of the original balance due payment?

This is a portion of the Amended Return (Form 1040X). You will want to make sure you answer the questions correctly about if you made your payment already or not, then the calculation will be correct based on what you have or haven't paid.