ok for anyone who want to know this is the best option I can find and by far the least annoying to users.
download: https://code.google.com/p/php-mobile-detect/
and write this in your page or however you wish to do it. I use a mix of my own and bootstrap styling on my webpages for the classes.
<?php if($detect->isIOS()) : ?>
<div class="alert alert-block alert-success" id="mobileApp" style="position:absolute; left:10px; top:15px; z-index:1003; width:910px; text-align:center;">
<button type="button" class="close" data-dismiss="alert">Close</button>
<div class="span3"><img src="imgs/if.png" width="125" height="125"></div> <div class="span5"><h3>we are on the go!</h3></div>
<div class="row">
<div class="span4"><h4>Download our app TODAY!</h4>
<a href="#" class="btn btn-success btn-large " style="color:#fff;">
Download iPhone App
</a>
</div>
</div>
</div>
<?php endif; ?>
you can repeat this for the android with
<?php if($detect->isAndroidOS()) : ?>