Relation Between Drupal Commerce Line items and Products
It sounds like you are confused.

Short answer:
Line items has a reference to a product.

Explaination
Line items are only used when you add something to your order (cart), they have a relationship between the order and the product and hold data like price quantity, but can hold additional data, like the address (in case of subscriptions), which a unique each time you buy something.

If you have product attributes like size or weight, you probably want to store this on the product, since a products with different sizes and weight should be different products (A S size t-shirt is not the same as a L sized t-shirt).

So it really sounds like you are doing this the wrong way.