booked with bookings.com for all of my trips to thailand (krabi twice, bangkok, hatyai). so far so good, and the payment whether 100% or not is based on what the terms and conditions of that particular hotel is. stated on the section before you make payment.

the thing about bookings is that some hotels that is on Agoda, isn't available on Bookings.. so i guess you'll have to really survey before placing your bookings~