there is not such a shield in fritzing program, so I just put that one.
I have tested it with separate power supply with removed jumper. However chip heat up real quick.
Okay I managed to borrow two Lithium Ion batteries, one with ~7V and another with ~8V. I used them to separately power supply both microcontroller & sensors and DC motor driver and it works fine now. Having 7V connected to atmega2560, Vin pin, wont cause any problems to the microcontroller?