Measure the flat surface area of the pencil box.

Cut your Lego plate to those dimensions. If you are making multiple boxes, make sure to check which way will give you the most pieces from one plate before you start cutting. In my experience, base plates cut with regular scissors, but if you are having trouble try using a utility knife.

Hot glue the Lego piece to the top of the box.

Repeat the process with the inside of the box. This gives them a place to build and a place to play with more freedom on top.

When they are done playing, all of the pieces can be stored inside the box.