Service tax will be paid by Flipkart and not you
Suppose you make sales of 100000 through Flipkart
Flipkart charges 6% commission i.e. 6000
It will charge Service tax @ 15% i.e.6000*15%=900
Flipkart will pay you 100000-6000-900=93100
In this case,Flipkart will pass entry
Bank Dr 100000
To Customer 100000
Vendor Dr 6900
To Commission Income 6000
To Out put Service tax 900
Vendor Dr 93100
To Bank 93100
Customer Dr 100000
To Vendor 100000
In this case,you(Vendor) will pass entry
Flipkart Dr 100000
To Sales 95238
To Output Vat 4762
(Assuming 100000 inclusive VAT 5%)
Bank dr 93100
To Flipkart 93100
Commission Dr 6900
To Flipkart 6900
or
Commission Dr 6000
Input Service tax 900
To Flipkart 6900