@MLDV
I believe you are looking at two different areas and they are only related by the client but not by their transactions. When you are applying payment to an invoice then those values are reflected in the Transaction of the client. While Opportunities are a separate area and does not related to the Transactions.
Under Customer > Edit Customer > Transaction section will contain all record that includes invoices, estimates credit Memo and payment. While Opportunities contains items like discount and/or coupons and payment will not be reflected here.
I hope this helps clear up any confusion.