You have to respond to the IRS notice that you received. Did the notice say that you can include an amended return with your response? If not, it might not be necessary or helpful to amend. If you do prepare an amended return, send it to the address specified in the IRS notice, together with the other parts of your response. Do not file the amended return separately.
But the better approach, as DoninGA suggested, would be to go back to the CPA who prepared the return, and bring the IRS notice. The CPA should prepare a response to the IRS notice for you, and prepare the amended return if needed.
