Close outstanding receivables/payables together with subsequent payments use the function for manualy closing. To link payment to receivable both document types must include matching subjects, accounts and currency. For example, in this case Alpha Trade has an outstanding local currency receivable on the account 1200, plus its subsequent payment in a foreign currency.

The subject already settled the payable, but the document is still displayed among the outstanding items. That is because the payment has not been linked with the invoice to which the payment is related. When the invoice issued and payment received have the same linked document and are balanced (as here where the subject already settled the invoice), the document will not be displayed among outstanding items anymore.
One way is to provide invoice ID in the Linked Document field already when posting payment. It will close subsequently. This can take up much of your time if you have several invoices opened, though. That is why PANTHEON allows you reviewing outstanding receivables/payables, their subsequent payments and their closing.
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You must be aware that the program looks up only those receivables/payables and payments that are linked to the same subject, to the selected account and selected currency. Amounts that have been posted to different accounts or in different currencies will not be displayed.
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Simply link receivables and payments in the Close | Manually module and close them. Clicking Close button the selected receivable and corresponding payment are linked up and enters linked document of invoice to the journal entry. The document is closed.

Related topics:
For a general description of functions see: