For each different size, color, weight, ... you have to make a new product entity with the desired fields.
Example:
In your store you have 3 different kinds of shirts:
1 shirt Small black
1 shirt Medium blue
1 shirt Large blue
In the store:
Create 2 required fields, color and size.
Create 3 different products, for each different attribute another product.
In product display:
Then create product node in content type 'display_product', add link to referenced product.
Put the SKU of the 3 products in the referenced product field.(value has to be set to unlimited)
When you look to the product node, you can see the size has a dependencie on the color,
if you want the color to have a dependencie on the size, switch the fields in the manage field settinges on the product type display in the store.
For products where 1 attribute is the same for all the product entities (example: weight, brand, type of clothing) create extra fields in the 'display_product' type.

Good luck!