@Ray303: You can control almost all zencart features, but you'll have to do it manually. You'll have to edit the appropriate _config files in your includes/config_sites folder.
In other words, if you want your site1 NOT use storepickup module you'll have to edit your shop1.com_config.php and add the following line:
Code:
define('MODULE_SHIPPING_STOREPICKUP_STATUS','false'); //Enable Store Pickup Shipping
By adding that line, your shop1 will not use storepickup module. You can do that for almost any other module/feature you have installed, you'll just have to use the appropriate command...
Note that you're NOT changing any template files whatsoever. ALL modules/features are controlled from the _config.php file! Have fun!