How do you prevent duplicate sales entries...

The problem I am trying to overcome is when I invoice a client, and they pay through the PayPal link on the invoice it enters that into the system. When my PayPal transactions get downloaded to Zoho books... to be matched... there is not an option to match that transaction as being the payment for the invoice.... so it becomes a duplicate entry that cannot be deleted.

Help, I'm new to Zoho and really like it because of the PayPal function. I haven't found a system that works as well as this does for me. This is my only snafu!