As Licensecart mentioned, the Payment Received email template is a receipt of payment, but does not include any invoice(s) as attachments, if any were paid with it, partially or otherwise.
The only reason I can think that the amount applied appeared as twice the value you entered is if you had paid it twice. For example, perhaps as you were recording a payment, that invoice was paid via cron from a loose $100 credit, or the client happened to make a payment at the same time for the same amount you were recording. In any case, it's best to look at the Transactions table to see where the payment originated.