Where you have 2 sets of products for which a different delivery charge should be applied, we recommend the following solution:
1. For all products from Product Set A specify a zero weight value.
2. For all products from Product Set B specify a non-zero weight value, e.g. 0.002 kg.
3. Next you will need to create an Order Weight shipping method type so that products with a specific weight are charged differently.
When creating a shipping method you could create the following ranges:
0.000 - 0.001, cost value - the cost which will be applied to the Set A only
0.002 - 5.000 (a significantly greater weight value, just in case a big number of products from Set B are added to the cart), cost value - the cost which will be applied to the Set B only
For more information on how to work with shipping methods, please refer to: Working with Shipping Methods