Snälla would not be used like that, unless it’s more of a desperate plea and not a polite request. You could either move it to the start or replace it with tack or even do both. Probably would also be better to use på or vid insted of i. Stolar should also be stolarna as you are talking about a specific set of chairs(the ones in the classroom) not just any chair anywhere.
So in conclusion: “Snälla stapla stolarna vid slutet av dagen, tack”
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