Slightly depends on your version. For most for versions there the skin CSS.
If you are wanting to change the bootstrap types in version 10 that would depend on the view. For example if you want to change a button from btn-primary to btn-warning. You could make changes to \Web\Views\ShoppingCart\_AddToCartForm.cshtml .
For versions older than 10 to add or modify the add to cart button html you will need soucre to edit the button html.
Hope that helps.