We've updated the filter options for banners. From version 4.04+ you can now use the same Customer-based filters here that you're already accustomed to using in Layers.
With each filter, you can use a checkbox to exclude filter values, so that the banner applies to all users except for those listed.
For users with multiple accounts, you can specify whether only the user's current customer code is checked, or validate against all the customer codes that user has access to.