We are looking to charge a fee for one time ACH loan payments that are requested by calling our customer service dept. We would debit the customers account at another bank and credit their loan with us. We would record the ach authorization over the phone as well as disclose the fee during the conversation with the customer. Should the fee be a separate ACH entry from the payment amount debited?

It really is more of a business/operational decision. If for some reason the customer does not have the money in the other account, do you want to set them up for another $35 OD fee for a $3-5 service fee?

I'd also look at CFPB Compliance Bulletin on Phone Payment Fees regarding disclosing fees for various payment options.

I'd consider creating two separate ACH Entries; one for the actual loan payment amount and one for the fee. This not only makes the accounting easier and the account statement transaction disclosures clearer, it might also prevent a loan payment from going past due if the account to be debited had enough funds for the loan amount but not enough for the loan payment + the service fee.