include exception inside theme for empty widget area

I am not exactly sure what you’re question is but I think you are looking for something like this, mostly cribbed from the Codex:

if ( is_active_sidebar( 'sidebar-1' ) ) { ?>
    <ul id="primary"><?php 
        dynamic_sidebar( 'sidebar-1' ); ?>
    </ul><?php 
}

If the sidebar is not in use, no markup will display. You could add an else is you want:

if ( is_active_sidebar( 'sidebar-1' ) ) { ?>
    <ul id="primary"><?php 
        dynamic_sidebar( 'sidebar-1' ); ?>
    </ul><?php 
} else {
    <ul id="secondary"><?php 
        // some other code ?>
    </ul><?php 
}