When you add or edit a material through the Catalog Manager, the custom material is saved with the catalog, and is only available when editing elements in the catalog. If you add or edit a material when editing an element that has been inserted in your drawing, however, the customized material is only available in the current project when editing the properties of inserted elements. The materials library in the catalog remains unchanged. This is because the materials library in the catalog is separate from the materials library in the current drawing.
The reason that there is a project-specific materials library is so that any materials used in your project are always saved with the project, making it possible to share your project with others and always maintain your customized materials.
If you want materials that you have customized in your catalog to be available in your project-specific materials library, or vice versa, you can use the Transfer tool to save the custom materials to the external materials library file (materials.mlb), then import the custom materials from the library file into the other materials library.