Dear Sir,
In fact there is no need to refer to Rule 2A of determination of value rules, 2006.One should refer to Rule 2A only where contractor is raising a single invoice containing charges for supply of goods as well as for labour. In that situation only Rules 2A would come in play. In your case contractor is raising two bills (not charging gross amount for works contract) one for sale of material and other for labour charges. in invoice for supply of goods he has already provides on what value he has paid vat and that value of goods shall be treated at value of goods for determining value of goods portion in a works contract. In fact clause (c) of explanation to Rule 2A(i) provides that where VAT or sales tax has been paid on the actual value of the goods then such value of goods shall be taken to determine the service portion in execution of works contract.
what is taxable is service portion in the execution of works contract and Rule 2A of the determination of value rules provides a mechanism for valuation of service portion in a works contract where it is not available. in your case contractor is already issuing saparate invoice for service portion. so no need to refer rule 2A.
you simply need to pay tax on the labour charges. if your service provider is individual, huf or partnership firm and you are a business entity registered as a body corporate, you will be covered under partial reverse charge machanism and both shall have the liability to pay tax to the extent of 50% by SP ad 50% by SR.
Regards
Akash deep