Hi Amit,
Where the company is paying service tax as a receipient of service, they will file the ST 3 returns as the receipient of service. Your client who is a transporter need to tick the check box in his consignment note the person who is liable to pay service tax. In this case if the company is paying service either as a consignor or consignee and the transporter should tick the check box accordingly. Here the liability of the transporter is over and he need not take any registration nor required any return filing.
In other situation, where the transporter registers himself as a service provider has to file the ST 3 returns. In such case, there are 2 possibilities. First possibility is he will charge service tax in his invoice and tick the "transporter" check box in the consignment note. In other case, he will just tick the consignor or consignee check box in consignment note and will not charge any service tax in the invoice. In first case, the value of taxable service received will be the gross amount received towards the service. In second case the value of taxable service will be Nil as the same will be shown by the receipient of service. No need to show in any other column like exempted other than export etc.
I hope your query will be solved on above reply.