With Receivables the invoice batch includes the cash invoices, however, I notice that with receipt from Order Entry it is treating the cash invoices as a cash batch. Is there any way to have it still view the batch as an invoice batch despite the fact that there are some cash invoices?

Sorry, no. OrderEntry separates out the cash recorded in OrderEntry into a separate cash batch. The documents are linked however, and will be automatically matched when the batches are posted.