If I'm understanding you correctly, you want to hide a category from the nav menu but have it show up as a sub-category in the content area, such as in a category grid. This isn't supported out-of-the-box, but it shouldn't be too difficult as a customization. One thing you will need to decide is whether you want to change that behavior across the board or offer it as a per-category option (e.g. "hide this category in menu" checkbox in the admin).

I think you will have a tough time making this change without modifying the core source code. It sounds like you will need to add a column to the bvc_Category table in the database and then add the corresponding field to the business object (BVSoftware.Bvc5.Core.Catalog.Category). Once this is done you will need to modify the menu control to look for the new field.