Hi,
You can do like that:
1. Create two warehouses via the menu System>Warehouses
2. Assign each warehouse to the different groups of products, either by editing the products, or using mass actions (menu System>Mass actions, to assign them automatically).
3. Duplicate your shipping methods, one set for each group, and configure the corresponding warehouses for the Shipping methods.
4. Edit your payment methods and assign them to the different shipping methods.
That way, on the checkout, the system will group the products per warehouse and each group will have its own set of shipping methods to select from.
When only one group of shipping methods will be available, only one payment method will be available.
When both groups will be available, the customer will have to select two shipping methods (with the shipping fees cumulated) and will be able to choose between both payment methods.
A simpler alternative would be to use the weight/volume restrictions of payment methods to group the products together based on their weight/dimensions.
So for example, you would have one group of products with a weight and no dimensions, and another group with no weight and dimensions, and then use the min/max weight/volume restrictions in the payment methods to have payment methods based on the total weight/volume of the products in the cart.
