I had a similar issue in QuickBooks desktop so hopefully this helps.  I changed the email address on my merchant account so that invoices were emailed from a new address and that worked great (click Merchant Service Center in left nav, Account>Account Profile, edit email in Contact Information section).  The problem was that when a customer paid, I still received "Payment received" messages to my old email address.  I searched and searched (including this posting), didn't find the answer and finally called support.  I spent an hour with frontline support and was finally escalated to the second line support who asnwered my question in less than five minutes.  Go to My Company in left nav and change the Email address under Company Information.  That is the email address where you will receive the "Payment received" messages.  Worked like a charm.  Best of success to you.