the Rate Lookup services do not not offer a way to break one item into multiple boxes.
probably the best way to account for this is to create a new cart column for additional shipping, this column will need to be in the products database as well.
For items that will ship in two boxes, add the cost for the second box.
Then in the add to cart buttons, bind the new shipping cart column to the shipping recordset column and create a new shipping rule>
subtotal For Any Column
if the column additionalShipping is > o
Based on column subtotal
subtoal of column additionalShipping plus 0