I just wanted to relay my experience with the new payment system. I set it up last week on the 18th for the three day interval. The first transfer got initiated on Saturday the 21st and I got the Amazon transfer email a few hours later. I got a confirmation email from my bank on Monday the 23rd at 4:30 am saying that the funds had posted to my bank account. With Amazon payments, my weekend transfers were posting on Monday mornings, so no real change there.
So, all-in-all I didn't have with any issues switching over to the new payment system. I was surprised because I thought that I would end up with problems. Anyway, that's how it went for me.