I can tell you how I’ve done.
In <?php /********* Featured Section. *********/ ?>
<?php $loop = new WP_Query( array( 'posts_per_page' => 1,'post__in' => get_option( 'sticky_posts' ),'post__not_in' => $no_duplicates, 'ignore_sticky_posts' => 1 ) ); ?>
changed in
<?php $loop = new WP_Query( array( 'posts_per_page' => 1,'paged' => $paged,'post__in' => get_option( 'sticky_posts' ),'post__not_in' => $no_duplicates, 'ignore_sticky_posts' => 1 ) ); ?>
In <!– Begin categories. –>
<?php $loop = new WP_Query( array( 'cat' => $category, 'posts_per_page' => 4, 'post__not_in' => $no_duplicates ) ); ?>
changed in
<?php $loop = new WP_Query( array( 'cat' => $category, 'posts_per_page' => 4, 'paged' => $paged,'post__not_in' => $no_duplicates ) ); ?>
Then I added <?php leaf_pagination(); ?>
before </article><!-- .post-home -->
For this very last thing I don’t know if that’s the right place for you too, because I made other changes (not pagination related) removing some code. Anyway this isn’t a problem.
<?php leaf_pagination(); ?>
it’s a ready function included by the theme author, so just put it where you want to visualize numbers pagination, after more article section in your case.
You must work on the child theme via FTP, and if you mess up delete the copied file in your child theme and redo over again with a new copy until you find right position with no syntax errors.
Sorry but I don’t understand the second part of your question