All payments that are recorded in Xero will automatically be matched against the corresponding sales order in Shopify and will be marked as PAID.
Xero does not let the paid invoices be reconciled with bank payments and some users may choose not to sync payments if they are reconciling the invoices with bank payouts manually.
Select Yes to record the transaction payments for your order in Xero. All the payments including partial payments will be recorded and mapped against the appropriate sales order in Xero.
Choosing No will leave all the invoices UNPAID and they need to be marked as PAID manually.