What do you mean by adjust the cost during payment? Are you planning to recover the cost of the materials from the amount you have to pay to the vendor?
The standard scenario will be you create a PO to the vendor for his service and pay accordingly. It will be a part of you agreement with your vendor that you will supply the raw material. There is generally no question of deduction of the cost of raw materials from his service charges.
Create a service Po with account assignment P against your WBS. When supplying the goods, modify movement 221 in OMBW to make PO optional, enter this PO number when issuing the goods for tracking.
Both your service and materials cost will load onto the project. You will also have a track through the PO, to know for which purpose these goods have been supplied.