Yes, you will want to file a Form 56 with the IRS as trustee. You will need to file a separate Form 56 for the decedent and estate because they are separate taxpayers.
You can file the Form 56 with the tax returns. You would have to file them earlier if you need to take any actions with the IRS before the tax returns need to be filed. (An example might be if you needed to contact the IRS for information on the taxpayer's account before the tax returns are due or if you need to file for an extension).
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