Multi Theme Support

Currently we have multi-store license and multi-store setup with different theme for each store. Do we have support for different Javascript googlehelper.js file for different theme as we might want to do some changes specific for one theme but not on other theme.

For Example, we want to change the structure
$('.add-to-cart-button, .product-box-add-to-cart-button') to some other selector in jquery

No, plugin doesn't support multi themes JS files.
I advice you to add the new custom css style for this add to cart button for all themes and use it for only for JS selector.
Example

$('.ee-add-to-cart-button, .ee-product-box-add-to-cart-button')