You should be using domain\username. I know there are some modifications around that add the domain name to the data entry automatically but these are not supported :)
Prerequisite is that AD users can log in in the first place. If you have trouble figuring out which domain/user format to use, it should be the one in User.ADLoginName field in the database.
Note that for pass-through authentication to work you would have to be using short domain name anyway, FQDN will not work for that.