The entity API offer us a few theme suggestions that we can use to override how our entities look.
Let's say that you entity type is called "post" and one of your bundles is called "blog", and that you have created an entity with id 1. The following theme suggestions are available:
post.tpl.php
post__blog.tpl.php
post__blog__teaser.tpl.php (teaser is a view mode)
post__1.tpl.php
This offered you a very fine grain level of customization to theme things according to your needs.
To use these tpl.php files we need to let drupal know through the theme hook.