Contacting the IRS is your best option to confirm they have received the payment and that it is applied to the correct tax year. If the IRS does not apply it to the correct year, then when you file your tax return, the payment may not be matched to the correct year and it will cause delays in processing your return.
General procedural questions shows what you need to do before contacting the IRS but it also has steps of how to review your account and check the payments.
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