Composite Service Tax working under work Order

Dear Experts,

   Need guidance on calculating Service tax under work order.

Example,

Raised Work Order, with 100 lines and the service tax will be calculated on  the work order amount + Free of Cost items ( issued to the vendor at market price from company inventory not part of Work Order issued) 

the difficulty arises capturing the service tax amount which is recoverable part.

Please guide, if you are working on such cases.

Thanks

Sachin