If you use journal entries to pay the invoice the invoice will never show as being paid, you must make the payment using the receipts module or the payment will not be linked to the invoice.  You should test this on a test copy of your database to confirm!  You may have to set up one of the temporary accounts for stripe to allow the funds to show as a bank for it to be available in the payment module.  I am not an accountant so I may not be using the correct terminology!

Hi.  Thanks for your response.  Thank you for the idea of the test database.  I will see if I can figure out how to make that work.  I do realize this all goes through the A/R module.  My concern is more on how it goes through the module and what accounts are effected.  

Hi.  Thanks for your response.  Thank you for the idea of the test database.  I will see if I can figure out how to make that work.  I do realize this all goes through the A/R module.  My concern is more on how it goes through the module and what accounts are effected.