Sir,
Job work will be treated as service unless it amounts to manufacture under Section 2 (f) of Central Excise Act, 1944.
Under Rule (4 A)of Service Tax Rules1994 where an assessee has paid to the credit of Central Government any amount in excess of the amount required to be paid towards service tax liability for a month or quarter, as the case may be, the assessee may adjust such excess amount paid by him against his service tax liability for the succeeding month or quarter, as the case may be. However, under Rule 4B of Service Tax Rules, 1994 the adjustment of excess amount paid, under sub-rule (4 A), shall be subject to the condition that the excess amount paid is on account of reasons not involving interpretation of law, taxability, classification, valuation or applicability of any exemption notification.
Therefore you cannot adjust excess service tax paid on franchise service towards payment of service tax payable on the job work done by you since you have not at all paid service tax on the job work done by you and moreover you are entertaining a doubt whether job work done by you amounts to manufacture or service which is question of interpretation.