Glue an envelope in the back of student notebooks for when they have small pieces of things they are working on but are not ready to glue in their journals yet. I would glue the envelope in the front though.
Simple solution to all your dice problems! Stick two dice in a small tupperware container. Have the children shake the container and look at the dice. No "throwing" dice or losing them either. I will probably use foam dice as they are noiseless.