You do not enter Form 5564 in the program.
"If you agree with the changes, sign the enclosed Form 5564, Notice of Deficiency - Waiver, and mail to the address shown on the notice."
Per the IRS website: "We received information that is different from what you reported on your tax return. This may result in an increase or decrease in your tax. The notice explains how the amount was calculated and how you can challenge it in U.S Tax Court."