Xero does not support applying overpayments / credits to invoices via their API, therefore you need to manually apply overpayments / credits that have been applied to invoices in Neto to related invoices in Xero.
Neto provides a management report / console so that you know exactly what overpayments / credits need to be applied to what invoices in Xero.
You can access this console by going to Xero > Credits Pending Allocation.
This will display a list of credits / overpayments that need to be applied manually in Xero.
You will need to click on the Re-generate button to display the latest data. The report will take a few minutes to generate.
For instructions on how to apply the credit to invoice, read the article Allocate credit to invoices or bills.
Once you have applied the credit, you can mark the credit allocated on the report by selecting Mark as Allocated.
To mark invoices in bulk, select them on the left and then scroll to the bottom of the report and select With Selected > Mark Selected as Allocated.