WCT is applicable where the purchase of Material & Labour (both) are included in Party Bill, and your company & the party belong to the same state (say Gujarat). WCT Rate vary from state to state.
In gujarat, it is 0.6%
In Delhi, it is 2%(not sure about any update as i am from Gujarat)
In Gujarat, If your company has given a work contract to a party, then WCT is to be imposed @ 0.6% of the value of the invoice.
There is a separate challan to pay WCT. It is to be paid in Sales Tax Authority just like VAT. You have to provide monthly Declaration to the party, & an annual certificate.