Doesn't make a difference whether you have related posts on the side or bottom. That's preference. Showing related posts keeps readers on your site. It also helps Google understand the context of your articles. Search engines likely understand the difference between body content and template content (header, footer, side navigation, etc). If having related posts to the side and below the content looks ugly, just show it on the side. Either way it's boilerplate that would be treated with less value than your body content anyway.
Links at the end of an article get a lot of clicks, assuming you have good content and people make it that far. That's why it's a popular spot for monetization.
The way I look at it, do whatever makes your page stickier, i.e. whatever makes the user stay on your website longer. This reduces the chance of pogo-sticking back to the search results and increases the time they spend on your website. Both are good for user experience which in turn is good for SEO.