The one in /etc/php/7.0/apache2 is the base configuration that PHP uses. By default, PHP does not read php.ini files located in your website’s document root. You can configure Apache to use a different file by adding PHPINIDir /path/to/directory/containing/it to its configuration file (not the virtual host config), but you usually wouldn’t need to do so.

So, in short, only the one in /etc/php/7.0/apache2 matters. The other one is not used. You can verify which one is being used by placing a file containing the following and then browsing to it:

<?php
phpinfo();