For online Sales,also rules are same
If Sale within State,then Vat is applicable
If Sale Outside State,then CST is applicable
If Vat Rate is 5%,CST Rate will also be 5% as we are selling to Unregistered Dealers
You can pass combined entry for whole day/month sales as follows
Bank Dr/Flipkart Dr
To Sales Local 5%
To Outpuit Vat 5%
or
Bank Dr/Flipkart Dr
To Sales Central 5%
To Outpuit CST 5%