@Joan, where do payments for factored receivables get sent; to the factors bank or to the clients bank?
If they are received directly by the factor or via a lockbox, then set up a new bank code for the factored receivables and use this bank code to report the payment receipts. Tie the bank code to the factoring liability account. As each payment comes in, record the amount received less the factoring fees to the bank account and then record the balance to the factoring fees account.
If the monies are received directly from the customer by the company and the monies must be remitted back to the factoring agent, consider either setting up the factored customers in a separate division or creating a UDF to apply to the invoice to note that it is a factored invoice. Then, when you are processing the receipt of payment, you can make record additional lines in cash receipt entry to GL lines to record the additional offsets at the time of receipt.