Hi chrisntoukas,
One way you can do this is by following these steps:
1. Create a child theme;
2. duplicate single.php from the parent to the child (create a file called single.php and copy all of the content from single.php in the parent theme into single.php in the child theme);
3. In single.php in the child theme, find the place where you want the banner ad to appear and add the following snippet
<?php if (in_category ('category1')) { ?>
<div class="banner-ad">
This is a banner ad
</div>
<?php } ?>
On the basis of the code above, if we’re viewing a post in category 1, a banner ad will be displayed.
Obviously, you will adapt the category slug (the category name) and the mark-up for the banner ad to your own needs.
I hope it helps.