" once I make this payment online, should I reflect this payment anywhere on 1040x? or just keep 1040x as it is (showing $100 tax due)? "
No. When you make an online payment, the IRS knows that you paid. The tax liability and payment information is aggregated in your tax account. A transcript of your tax account is available online:
https://www.irs.gov/individuals/get-transcript
Of course the tax liability from your amended tax return won't be present in your tax account until they process the amendment, so the payment will typically be in your tax account well before the corresponding liability from the amendment shows up.
