I figured it out. And I love wordpress and it’s forums…
It was simple enough to create a category called ‘featured’ or whatever, then include that category name into the slider $args in the index.php.
Then further down in the same file, filter that same category out of the post listing (thanks to http://techbrij.com/exclude-posts-by-category-name-from-home-page-in-wordpress for providing a nice little piece to use category name instead of category id on the exclusion.
And to preserve the template, I already had a template child I dropped the new index.php into the child folder and it works.
