Hi Samantha,
When editing either an Order or an Invoice in OrderEntry, there is a Payment button from which either partial or full payments can be applied. There are also fields that can be included with Order Confirmation or Invoice specification forms so that this payment information can be printed, along with a calculated amount owing.
There are some rules regarding entering payments in OE, such as that they don't appear in Customer Transaction lists and statements until the invoice is posted and retrieved into Receivables. To ensure that this process, or something else, would meet your requirements, it may be useful to discuss with your Adagio consultant.
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Regards,
Softrak Tech Support