Analyze the book collection for patterns. You may find many are from a particular author, or share a common size or spine color.
Use one of the patterns to set up the books for aesthetic appeal and ease of reference.
Place the books by category on a shelf. Measure how much room you will need for each category. This may involve some trial and error to find the system that works best for you.
Break up some of the redundancy of hardcover book spines with other items to bring visual interest to the shelf. Bookends, small statues and figurines, toys and other items contributed by the child may enhance the look of the shelf and help divide the categories.