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When you set up design layer viewports you have the option to choose all of the classes that you want to be visible, or you have the option to use the current documents class settings. You may be confused by what this really means.
What this really means is that the design layer viewport will use the classes visibility that you can control through the Navigation palette. This gives you the advantage of using the visibility tool to turn off classes and other design layers that you don’t want to see. When you return to your design layer viewport, those classes will be invisible.