For the payment of the service tax it is always advised to make a payment by cheque rather than cash, as it is accounted as white money and the white payments will be helpful for you from taxation point of view in future and when you will be planning to sell your property. Don't forget to ask your builder to provide you a receipt when you make him a payment by cheque
When you buy a flat you buy two things from the builder 1. Undivided Land of Share and 2. The flat. Both VAT and Service Tax as on Jan 2013 ...Service Tax @ 12.36% on 25% of BASIC Price ( if Land Cost is included ) otherwise 12.36% on 33% of Basic Sale price ) need to be paid on no 2 and not on no 1.