As the case suggests, You are working in Rule 6(3)(ii). Section has prescribed the method of calculation of cenvat credit to be availed. and Explaination 2 to this section provides that you can not avail credit of those services and goods which are used exclusively for exempted services.
Now if u have used the service in relation to the service which is exempted u can not avail credit of the amount paid by u. and if u have used the service in relation to the service which is taxable or in relation to both the service, you can avail cenvat credit only to the extent of the amount derived by respective percentage. It doesn't makes a difference whether u paid the amount of service tax in cash on input service.
Regards
Rajesh Ahuja