I use Bank of America.  My bank is linked, and the transactions have no problem showing up in QB.

I get a notification when an ACH payment is made via the invoice payment link.

The payment is then attached to the invoice, and the invoice shows as paid.

When the payment is deposited, it shows up in my BOA account transactions.

However, I am unable to match it to anything.  As I mentioned, the invoice shows paid.  When I click on the payment, it shows it's paid from the "Quick Books Payment Bank". 

When I select "find match" under the Bank transactions, neither the original invoice nor the payment show up as options to match.  I can only categorize it or transfer it.

Furthermore, I am unable to edit the payment because it is done by quickbooks and there is no option to change the payment method marked "quickbooks payment bank" nor edit the deposit to "undeposited funds".

I am attaching a screenshot showing how Quick Books (not I) logged the payment.