What best practices should be followed when implementing pop-up messages in PHP to avoid navigation compromise?

When implementing pop-up messages in PHP, it is important to ensure that the messages do not compromise the navigation flow of the website. One way to avoid this issue is by using JavaScript to display the pop-up messages instead of relying solely on PHP. By using JavaScript, the pop-up messages can be displayed without interrupting the user's navigation experience on the website.

```php
// PHP code to set a session variable for displaying a pop-up message
<?php
session_start();
if(isset($_SESSION['popup_message'])) {
    echo "<script>alert('" . $_SESSION['popup_message'] . "');</script>";
    unset($_SESSION['popup_message']);
}
?>
```

In this code snippet, we are using PHP to set a session variable for the pop-up message, but the actual display of the message is done using JavaScript. This helps to ensure that the pop-up message does not interfere with the navigation flow of the website.