You could use the following and it should do exactly what you want by checking the value of $loop->current_post
.
<?php $loop = new WP_Query( array( 'post_type' => 'work','posts_per_page' => '-1' ) ); ?>
<ul id="carousel">
<li>
<ul class="inner-items">
<?php while ( $loop->have_posts() ) : $loop->the_post(); ?>
<?php if( $loop->current_post && !($loop->current_post % 6) ) : ?>
</ul>
</li>
</li>
<ul class="inner-items">
<?php endif; ?>
<li>
<?php the_content(); ?>
<?php the_post_thumbnail( 'work-thumb' ); ?>
</li>
<?php endwhile; ?>
</ul>
</li>
</ul>
2
solved Insert html after certain amount of posts?