The folders in BaseCamp are meant to be one "flat" collection and not really the same as the way you'd use them in say Windows Explorer. A different way to think about it is having each one being a unique "filter" of the items in My Collection.
For example you could have the same waypoint in every single one of those folders. Lets say call this waypoint "Home". If you made any edit such as say adding a picture of your house, it would be show when you clicked on Home in any of your folders since there's really only one waypoint that is "Home". It just happens to be included in each filter (folder).
