We will close simultaneous 1st and 2nd mortgages to refi an existing mortgage and consolidate other debt. The 1st mortgage won't fully payoff the existing mortgage and other debt, thus the need for the 2nd mortgage. In using the alternate CD for the 1st mortgage, should the funds for the 2nd mortgage be shown in the Payoffs and Payments table?

You could. I think you meant "funds from the 2nd mortgage" and not "funds for". Just like you could reflect the amount transferred to the first lien on the 2nd lien disclosures.