By default (if you don’t add related_posts() to your theme, but instead keep the “automatically display” option on in YARPP settings) YARPP will simply append the related posts display HTML to the content. Is that now what you want?
Sorry, I mixed up the title, my question refers to content.php and not to single.php.
I would like to create a YARPP section between the actual content and the comments. That does not work with the default configuration since the YARPP section becomes a part of the content section (article, post, whatever). If I add related_posts() to single.php, my theme gets mixed up …
Turning off “automatic display” and then calling related_posts() gives you the most control. You can move the related_posts() call around to be anywhere you want, so you should be able to do anything you want.