Is it possible to have magento in a subdomain but have the main index.php in the main domain.
So I have www.mysite.com and users come to this url when they click on a menu link eg shoes they are taken to store.mysite.com
Answer of your first question: Yes, it's possible, you need to edit index.php & find the line
define('MAGENTO_ROOT', getcwd());
change getcwd() to your sub-domain path
if you want to create a sub-domain store using magento following link could help you: http://www.crucialwebhost.com/kb/how-to-setup-multiple-magento-stores/
You may put your site subdomain/directory & main domain may use as landing page. add below code topmost of header.phtml
if (!isset($_COOKIE['firsttime'])){
setcookie("firsttime", "no" );// EXPIRE $getMegBaseUrl=Mage::getBaseUrl();
header('Location: '.'http://www.landing.com/index.php');
exit(); }
for landing page another directory/folder
if (!isset($_COOKIE['firsttime'])){
setcookie("firsttime", "no" );// EXPIRE
$getMegBaseUrl=Mage::getBaseUrl();
header('Location: '.$getMegBaseUrl.'landing/index.php');
exit();
}