OK - first question is do you have a copy of the Supply Contract, and if not you need to get hold of one. For compensation events (and there is a list of what would be a compensation event in clause 60.1) that only affect the quantity of goods and services being provided then the rates within the Pricing Schedule are used and the percentage for overheads and profit would not apply. For any other compensation events, there will be a quotation submitted by you identifying costs that will be incurred in terms of people, equipment, plant and materials included in the goods, work subcontracted by the Supplier and lastly transport. The fixed "overhead ad profit" percentage you declared at tender stage in contract data part 2 will then be applied to those costs.
You will find more information within the "Guidance Notes" that is a separate book. If you do not have these, you can buy the full contract set or simply the "SC contract bundle" using the following link at a cost of £85 which includes the contract, guidance notes and flow charts: