If you have to accept online payments from your Indian customers, you need to have an Indian payment gateway A/c. Once an Indian payment gateway is set-up on your online store, your customers can pay you via credit / debit card or net-banking.
To learn more about Indian Payment gateways, checkout our review of Top Indian payment Gateways.
And yes, if you already have a payment gateway a/c, you can use that. We have integrated all major payment gateways.
Apparently, in this case, you won't be paying any 3% transaction fee to PayU payment gateway.