Hi,
1. There is two things to do here. First, edit the column "product_quantity" of the table hikashop_product of your database via your phpmyadmin and set the default to 0 instead of -1. Second, before adding the characteristics to your main product, set the quantity of the main product to 0. Then, when you save the product with the new characteristics, all the variants should have their quantity to 0.
2. No, changing the code for that is quite complex.
The best in that case is to put the total stock in the main product. That way, that stock will also be decremented as well as the variant when it is purchased and thus you'll reach 0 in the main product when all the variants stock is 0 and in that case the main product won't display on the listing.