The Issue is very Simple. You have to understand the Concept. Works Contract is of two types one Purely Labour. In this case no Indirect taxes involved. The principal employer will employer will treat the payment as contract payment and deduct Income Tax2% with Cess. On the other hand If it include material also you have to split the total value into three categories. (1) Material Component (2) Labour Component (3) Indirect tax say (VAT).
The first two categories will have cost element also.
For material again it will have two sections viz. Locally Procured and Purchased outside the state.
Your vat liability is only the relevant state act % on the addition you bill your Awaqrder on the Locally procured materials and for Interstate purchase Total cost including tax and Addition made with respective % of the respective vat act.
Inorder to claim exemption at actuals your books of account must be complete in all aspect elst at a fixed % as allowed by the local vat act. Derive % of profit add with the cost of material and work out VAT at the respective rates to determine your vat liability for that contract.