Thanks @Jessica_young 

When I do that the summary shows

1) the two invoices being marked unpaid

2) the two fees being deducted to from my bank acct

3) An invoice what will be created for the fee to charge to customer (it's blank).

I then go into the second payment and apply it to the two original unpaid invoices.  What do I do with the journal entry that it created?  In the customer payment window, the journal entry for $1,806.87 is showing like unpaid invoice.  In addition, both journal entries, $1,806.87 and $15, are showing up on our unbilled accounts report.  That report is a listing of anything purchased with a Customer:Job name and marked as billable.