"Smart Labels play nice with other labels and filters too. On the Filters tab under Settings, you'll find that these filters can be edited just like any others. From there, you can also edit your existing filters to avoid having them Smart Labeled or change whether mail in a Smart Label skips your inbox," explains Google.
In fact, when you create a filter, Google shows an additional option: category. You can choose from: bulk, forums, notifications, personal, promotions. The first three categories already have corresponding smart labels and all the messages classified as "promotions" are labeled "bulk". The "personal" category includes the rest of your messages.
Google's categorization algorithms aren't perfect, so you may find messages that don't belong to one of three categories, but they're labeled as "notifications" or "bulk". Use the "labels" drop-down to remove the labels that are incorrectly added and help Google improve its algorithms.