Cuboid syndrome is a change in the position of the cuboid bone in the foot and ankle caused by a sprained ankle. Usually the force of the sprain disrupts the nearby ligament allowing the bone to slip out of position.
The manipulation you are referring to is called a cuboid whip. It's done by bending the knee and putting the foot and ankle in a "toes-up" or dorsiflexed position. The patient is face down on a table. The operator's thumbs are on the bottom of the foot under the cuboid bone.
The knee is straightened while the ankle is pointed down. The operator turns the foot slightly inward and applies a thrust force to the cuboid. This action moves the cuboid bone back into its proper place. There may or may not be a pop. It's usually a painless manipulation.
An alternate way to do the same thing is called the cuboid squeeze. The foot and ankle are slowly stretched into a plantar flexed position (toes pointing down). When everything relaxes the examiner squeezes the cuboid with the thumbs putting it back in place.
The cuboid squeeze works best for people with cuboid syndrome from overuse. If the problem was caused by an ankle sprain, the joint manipulation is still the best way to go.