How to process auto Vendor Payments?

Just wondering how others are managing auto payments thru bank. Currently we have a couple of vendors who we have set up to pay automatically thru the bank. When the bank feed comes in how are you matching them. Are you just making an entry at that time or do you enter the bill as if you were going to pay by check?

For instance: Company Inv XXX - comes in for 150.00. These are set up thru the vendor company to pay when they become due. They send me an invoice but I receive nothing else until the payment is made. I then get the notification that the payment has been made. When we upload the bank feed the payment shows up but not the associated bill. Currently, I go in and say Make Payment. Then I can match. Is there another way to do this?