Proton can be found around lots of places. If he's not hanging out inside or outside of his dorm, he could be found wandering around campus just getting a good look at things and trying to find all the nooks and crannies of the place. He's looking for hiding places and any shortcuts here and there.

Or maybe he'll be in the cafeteria having a stare down with Nancy because that was an Ursaring with a laser eye and that blows his mind???

If you're lucky, you might catch him on the farthest side of the Kraken Lake with his Pokemon because he regrettably realizes they need time out of their Pokeballs too.

But basically, he could be anywhere