First thing is that you do not need to record the bancrofted fees in Accela at all, you could elect to record and collect them only through your agency financial system - they have to be in part as they are often interest-bearing. There is a payment contract between the applicant/customer and your agency typically, via Finance. Some level of 'payment plan' is outlined and agreed upon, and the customer typically is making those 'payments' to Finance as a more complex tracking system is often required for bancrofting.
However, if you do want to record bancrofted fees in Accela, you would assess the total fee, and 'pay' it with a BILLED exceptional payment method. This method does NOT show in your nightly cash reports for cash drawer settling as it is not actually CASH, so important note on that. BILLED effectively shows the fee as 'paid' when really it is just being billed to pay later. Another important note but does not apply here, any BUILDING surchargeable fees paid with BILLED are still due the State Surcharge whether actual CASH has been collected or not.
Then when the customer makes a payment to Finance, they would need to notify you, you would then VOID the earlier BILLED payment which makes the fee outstanding again, process a JOURNAL ENTRY exceptional payment type for the exact amount of the payment the customer made through Finance - then pay the remainder again with a BILLED exceptional payment again. Then 2nd time the customer pays Finance, you would void ONLY THE BILLED PAYMENT, leaving the earlier JOURNAL ENTRY in place (as that actual payment was made to Finance), process another JOURNAL ENTRY to reflect the 2nd payment they made to Finance, and so on, repeating this until they have FULLY PAID the entire fee with JOURNAL ENTRY.
A BILLED payment method is designed and intended to only be temporary, as a placeholder for actual payments to come - someone must manage these until fully paid. A JOURNAL ENTRY is designed specifically only to reflect payments made outside of Accela, in other systems that need to be shown in Accela for record keeping or tracking purposes. NEITHER show in nightly cash balancing reports as they are both really just placeholders of sorts, not ever really CASH payment.