You can store your email template in following directory
Create an view script like : /views/emails/template.phtml
<body>
<?php echo $this->var1; ?>
<h1>Welcome</h1>
<?php echo $this->var2; ?>
</body>
Please see this is already post on stackoverflow this might be helpfull for you How can I make email template in Zend Framework? and another solution also posted What is the best way to use Email Template in Zend/PHP