I believe I have resolved this issue by adding
into the first snippet of code that Charles provided.
So that it now looks like this:
<?php $recent = new WP_Query("cat=-55&showposts=12".get_theme_mod('featured_top_left')."&showposts=".get_theme_mod('featured_top_left_num')); while($recent->have_posts()) : $recent->the_post();?>
55 is the number of the "Featured" category in my setup. Now the Featured posts are showing in the FCG box, and all other categories below it.
Charles - thanks for your help!