Running more than one storefront can be very time consuming.  No one wants to deal with the confusion that sometimes occur when not having proper category structure. 

So what can I do?

We've found a lot of multi-stores set up their categories without planning ahead. This is not the best way to go about this. The best thing to do is to adopt a reliable method for setting up your category structure. This is to help reduce clutter and confusion.

Use Case scenario:

So lets say you have three stores. One of the stores is a sporting memorabilia store, another sells jewelry, and the third is a pet accessory storefront. You have some products that might cross stores, such as sport themed pet beds or a pendant intended to hold a picture of your lovable pet (or favorite athlete, I won't judge).

A solid way to break up these categories is to set up three categories in the root folder. The folder structure would look like this:

Root

    > Sports Memorabilia Main Store Category

    > Jewelry Store Main Category

    > Pet Store Main Category

Now that we have three main categories, we can put subcategories underneath to have an easier time managing your store. After deciding what the categories would be for each store, you can go ahead and add them under the store category.

Root

    > Sports Memorabilia Main Store Category

          >>Caps

          >>Shirts

              >>>Jerseys

          >>Giant Foam Fingers

    > Jewelry Store Main Category

           >>Necklaces

                >>>Pendants

           >>Bracelets

           >>Rings

                 >>>Diamond

    > Pet Store Main Category

             >>Pet Food

             >>Pet Toys

             >>Pet Bathing Products

So now its pretty easy to determine which product should go in where. But what about those categories that are going to be put on a multi store level? Lets put them in their own category structure!

Root

    > Sports Memorabilia Main Store Category

          >>Caps

          >>Shirts

              >>>Jerseys

          >>Giant Foam Fingers

    > Jewelry Store Main Category

           >>Necklaces

                >>>Pendants

           >>Bracelets

           >>Rings

                 >>>Diamond

    > Pet Store Main Category

             >>Pet Food

             >>Pet Toys

             >>Pet Bathing Products

    > Multi-store Shared Categories 

             >> Pet Themed Beds

             >> San Antonio Seahawks necklace for your cat

             >> Football Shaped Charm Bracelets

Sample Layout

At this point, you just need to go to your Active Catalog and attach the proper categories to the proper stores. If the category structure is set up with this method, you won't have any issues when you need to get rid of that "San Antonio Seahawks Diamond Necklace for your cat" category (who thought that would be a big seller?!?) without accidentally deleting the wrong category and losing other products.