Initially, when creating a Transaction Saved Search with these details: Criteria tab > Type = Payment and Main Line = True, the results should show all payment transactions from customers. However, if there are subsidiaries in the system, the record will include the prepayment amounts pertaining to its subsidiaries.
When Parent subsidiary pays the bills for the child subsidiary, the transaction type being used is the Payment. As a result, the report would show all the Parent company's customer payments in debit amount and the Prepayment for Child Subsidiary with negative figures.
To limit the result with the Parent company's customers only, make sure to add Subsidiary = Parent company in the Criteria tab.