Hi ttecha,
Thanks for the response and the update.
I'm glad one of your concerns is out of your plate.
For your other concern, generally, the Online Invoice Payment transactions automatically match bank transactions if set correctly. We will need to make sure that the option "Automatically match bank transactions to MYOB Bills and Invoices" is marked check from the Banking > Bank Rules window. For the other transactions that are still not matched. The Bank Transaction window will allow you to match paid invoices/bills by matching the transactions to the payment recorded instead of the invoices/bills recorded.

To help you match transactions, you can run the Transaction details report (Reporting menu > Reports > Online invoice payments tab). You can use this to help you match grouped payments in your bank feeds to invoice payments in MYOB Business.
Let us know if you require any further assistance with this.
Thanks,
Genreve