We are paying off a loan at our bank with another loan with purpose being a refi. We are also making the customer pay interest due from paid off loan upfront. Do we show this interest payment on the LE, and if so in what box should it go? We are showing the charge currently on the CD.

Which form are you using? It would just be in the payments and payoffs table on the alternate form.

bringing this topic back up. When we list the accrued interest under the payments and payoffs table, its deducting the amount from Cash to Close to the borrower. He is actually paying the interest separate in cash so the amount he is getting back is off the amount of the accrued interest. Is this ok for the LE or do we have a problem?

Yes, it's okay. His 'net effect' is being considered, much like an amount financed calculation.