It also depends on the age of the pupils. The older they are, the more likely it is they'll be allowed to choose where they sit.
Some of my primary school teachers would sit pupils of similar ability together so they could work on the same things. ("Red table, do this worksheet. Blue table, I've got a different one for you.") Secondary school teachers never bothered with this; in those classes we were all doing the same thing anyway.
You need to think about whether the students carry all their stuff to each class with them, or whether they have a desk in the classroom to store it in. In my secondary school it was always the former, but in primary school it was the latter, so we had to sit in the same place all the time.
Note, I didn't go to boarding schools, but I don't think they would be different.