I wanted guidance that if I want to add the Arduino uno or MEGA Board as it is to the PCB then how can I make safe connections of the pins with PCB?
Use pins and put the Arduino board upside down onto the pins.
Using the Arduino Nano or Arduino Pro Mini is also possible.
The Arduino Nano is ment for that, you make a socket for the pins and put the Arduino Nano onto it.
Using Nano seems to be great idea.
I want to keep the price to the lowest possible, Kindly guide me that will Arduino Nano be suitable or using ATMEGA 328P On PCB will be suitable? Which will be more efficient and less in price?
Also is the programming cable shipped with the Nano?
I think the cable is not included, but the Nano uses a normal mini-usb cable.
The Arduino Pro Mini is cheaper, but you need a serial-usb adapter to upload a sketch to it.
Using an ATmega328p chip itself on the pcb is also cheap and not very hard to do.
I can't tell what will be better in your situation. You have to check the prices and if you use the ATmega chip on the pcb you need extra time to design and test it.
Using ATMEGA might cost me around 6-7$ and Nano will cost be at least 14-15$
I can use the driver circuit as in the following link?
http://www.open-electronics.org/arduino-isp-in-system-programming-and-stand-alone-circuits/
Yes, but you do need a decoupling capacitor of 100nF at 5V and GND.
The minimal 16MHz circuit is: the ATmega chip, a crystal with two 22pF capacitors, 10k resistor at reset, and 100nF for the 5V.
The schematics for the Uno and Nano are online, you can have a look at those and learn from it.
It is possible to use the internal clock, so the crystal with the two 22pF are no longer needed. It is even possible to make that Arduino compatible, since the Arduino Fio and the LilyPad and the 3.3V 8MHz Arduino Pro Mini use the internal clock of 8MHz.
You can find all the information and schematics for those online.
When you want read an accurate analog value, you have to do more. See the datasheet for the inductor and extra capacitors.
Ok. Thank you 
Can you share a schematic that I should implement with ATMEGA328P that comes with Arduino UNO?
Arduino can be used as a standalone IC. You need not have to use your Arduino UNO board in the PCB in that way you can condense the size of your circuit. if you are using ATMega 328 you create the create the circuit in 16Mhz crystal oscillator.
Kindly share the complete circuit with 16Mhz crystal please?
