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There are several options for organizing your homeschooling home. Different approaches will appeal to different families. My kids generally like to have a say and help me organize, but they don't mind a surprise once in a while.
Some families have a homeschool room in which all or most of their learning supplies are kept. Others may have a shelf or cupboard dedicated to homeschool supplies. Craft shelves, such as those designed for scrapbooking are popular. Although you can buy school furniture designed for teaching and storing school supplies.
Although my family does have a crowded shelf and cupboard where we keep a hodgepodge of science kits, puzzle books, pencils, paper, etc., mostly we prefer to create thematic learning areas in the nooks and crannies all over the house.