It's in the last sentence. The rest of the sentences are for context because I know you all will love that, heheh.
Anyway, I presume it's about a boy transferring to the school and the teacher introduces him to the class while the main character takes her assigned seat. In other words, I think 席に着くよう指示した is being done by the main character, as the transfer student is getting introduced. If I'm wrong on this, let me know.
My main question, however, is what the よう is for here? Is the phrase perhaps translated, "She takes her seat as though it were assigned to her"? As in, the seat isn't specifically assigned to be hers, but she just kind of sits there each day and no one complains about wanting it. If so, why isn't it ように? Typo? This IS from an online submitted story, after all. Typos are possible, hah.