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"School Days" layouts are some of the most fun to create. If you want to use duplicate photographs in different sizes then create layouts that will allow you to do so.
Try using the small pictures as a border for your page or you can create a collage with your photos. A checkerboard border where you alternate your photos with squares of patterned paper or cardstock would make a cute, unique page outline. You can also cut the pictures into different shapes for an attractive photo collage. If you have the same photo on different pages and combine it with other photographs and designs it probably won't even be noticeable. This way you will be able to use your pictures (instead of disregarding them).