To clarify the Cash question where a payment is applied to an invoice in OrderEntry:

If you have the option in the OrderEntry Company Profile for Day End to create batches Directly in AR, then payments in OE are attached to the invoice in the AR Invoice batch. No AR Cash batches are created.

If the option in OE is set for Day End to create Retrieval batches for AR, then payments in OE are retrieved separately in AR as a Cash batch, and are not attached to the invoice in the AR invoice batch.

So if you require OE payments to be in a Cash batch in AR, then you could edit the company profile in OE to ensure the AR batch option is by Retrieval.