Use manipulatives to teach the underlying math concepts. Students must understand, for example, the concept of adding to something or taking away, or that fractions represent parts of a whole before being expected to learn the numerical operation. Manipulatives work best when they are used to support underlying concept and demonstrate how the concepts function.
Let students make, explore and play with manipulatives when teaching. Don't model how some manipulatives fit together and as students to mimic you. Place students in small groups of two to three and ask them to explore a concept. For example, let the students use any number of the manipulative to see how many equal groups they can get out of it. Give each group several round pieces of paper. Let the students cut the paper in half, and then help again to explore fractions.
Use the manipulatives to help with the basic operations of solving a number problem. Stack or sort them to help with multiplication facts that they are memorizing, for example.
Fade manipulatives out as students demonstrate an understanding of the underlying concept and are able to solve numerical problems. Lower-functioning students may need to use them longer or more often, but the average student will not need to continue to use them once they grasp the concepts.