I told my top program I would be ranking them number one. I think you can tell a program where you will be ranking them, but that they are not allowed to ask you, nor are they allowed to tell you exactly where you are being ranked. This, in theory, should prevent the applicant from being misled.
I'll save the thank you letters for those in family medicine. One of my attendings told me the last thing a surgeon wants is something else to read and to not bother with them.