Any question answered...

can't see any record of the drive. Is there a way to tell if the trip was logged and it will come out automatically? If I pay manually will they refund/not charge the autopay (assuming it comes out at the end of the month?)

Officially it can take "a few days" to register the journey and show it on your autopay account. If you make a manual payment, it will be deducted from the amount on your monthly bill. If you end up with a negative bill, they assume you're going to keep using the system so just roll it over to next month. You can theoretically get a refund of overpayments, but it takes months so not worth bothering unless you're never going to drive in London again.