The real-word name of those is baoding balls. They are not explicitly named anywhere on promotional material, so their name in the Tron universe is mysterious.
So, Clu only grabs those balls when Sam starts the final battle with Rinzler in the Disc Wars.
He starts turning them in his hand, stops suddenly, and then starts turning them in the opposite direction. As soon as he does that, the gravity on the arena switches sides.
So yes, he manipulates the game grid, but we don't know for sure if he is only able to manipulate gravity with them. There's some speculation that he also uses them to control Rinzler, as he seems to activate when Clu start to roll the balls. Maybe Clu could control the speed and/or aggressiveness of Rinzler by modifying the speed at which he rolls the balls. However, the first time Clu switches gravity, Rinzler turns his head to look at some control plate that is rotating, so he is not advised automatically of Clu's commands on gravity. Anyway, we also saw Rinzler obey a verbal command from Clu, so if they control him, they are optional.