It depends on how polite you can be.
Usually in a class room a teacher, or in army/office an officer is in command, and he can ask a student or his subordinate to "sit down"
But when a guest arrives at your home, you are polite to him and say "be seated".
"Seat yourself" is also used in the same manner when a person keeps standing and you politely ask him to seat.
Thus it depends more on the relations between the two.
P.S. : I am not a teacher of English, just someone who loves the language.
Student or Learner