The same way one goes back and forth around a room when they’re wiping its floors- with such an example, it’s easy to imagine the scene, isn’t it? For Lee, ‘one run’ around the village meant running through the entire village, every nook and cranny and road that the village had. It was a very simple-minded way of counting.
Of course, that meant that Lee’s path also included jumping over fences, hopping from tree to tree, and running over the roofs of closely packed houses. It wasn’t anything out of the ordinary, for a shinobi to take unusual paths like this through the hidden village. In fact, it was incredibly common, so much that the normal citizens no longer took notice of it.
So there wouldn’t be any landlords complaining about Lee running over the roofs. At most, one person would maybe send one complaint in the morning: “Some man with thick eyebrows was yelling ‘KUUAAA’ as he ran across our roof at dawn, he was really very noisy.”