No, it's one of the more difficult things to sort out... organising one's products into useful categories.
The feature that is really needed for this is product attributes and also a filtering menu system, neither of which are in the store.
In the demo store, this was a problem with the manufacturer and you'll find that each root category has duplicate manufacturers in them.
The only thing you can do now is think very carefully about your categories and come up with a system that works best with the least duplication of categories. For example, if there is a subcategory that is in every root category, then that category should probably be above the root.
The feature that is really needed for this is product attributes and also a filtering menu system, neither of which are in the store.
In the demo store, this was a problem with the manufacturer and you'll find that each root category has duplicate manufacturers in them.
The only thing you can do now is think very carefully about your categories and come up with a system that works best with the least duplication of categories. For example, if there is a subcategory that is in every root category, then that category should probably be above the root.