Hello,
I do not think you need new tax code nor delivery type as long as you do not need to declare this specific tax in separate posting of VAT register or declaration. I am out of Polish specificity for some time and I am not sure how you are going to bill your customer (customer order? Instant invoice?)
The easiest way to generate invoice would be to create customer order where sales price would be your purchase price and overhead/charge would be your margin - then you can apply zero % tax (or no tax) to the line base price, but regular tax code to charge = margin.
If I remember well VAT margin invoice does not contain tax rate or amount on invoice printout. I am not sure if standard invoice printouts in IFS can manage this.