I have some boxes but I like to line them up under my bed and keep them ready to shine. I try to rotate them equally.
Shoe Storage - Page 2
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Okay people, this is a 3 year old thread resurrected for this very specific question. Take a peek at the dates on the posts before responding...
To answer your question, I don't see any harm in having your shoes lying on their sides. Many people here store their shoes in the boxes to which you are referring. I choose not to, not because of potential damage, but purely out of laziness.