- Is it necessary to add 0.1uF to the all the VCCs of atmega? even if we are using 7805 which regulates the signal already.
Yes. You generally need bypass caps physically-close to the chip pins. That's true with most digital and analog chips. You might be able to get-away without them but then you might get "unexplained" problems/glitches. (There might be hundreds of bypass caps on your computer's motherboard and probably nothing bad will happen if you remove one of them.)
- Is it necessary to add RESET circuit on your pcb? (attaching positive voltage to the RESET Pin and all)?
No, but you might need a pullup resistor. Check the datasheet.
- Should i put some sort of DIODE on the input (which is 12V) ? i am using like 15A current for the whole circuit which include Pumps,LED strip etc so which diode should i be using if any?
A series diode with a capacitor on the Arduino-side can make a kind of filter to hold-up the voltage if turning-on a motor (or something like that) temporarily pulls-down the 12V supply. I'd probably use a ~1000uF capacitor.
- Is it okay to use pin 0,1 (RX,TX) or should i leave them and use other for the input or output?
It depends... If you are not using the USB or otherwise using those pins for programming/communication you can use them for whatever you want.
and why are people putting 1k resistor between controller pin and connector?
Someone else will have to answer that.
- can you please tell me the ways to burn sketch and boot loader into the atmega 2560? i just want names of that process and i will google all of them.
There is some information on [u]this page[/u]. [u]Here[/u] are some programmers from Atmel/Microchip.
…If you are going this-far in deviating from the standard Arduino hardware and burning your own bootloader you might want to skip the bootloader and all of Arduino stuff altogether and use an Atmel programmer and Atmel Studio development environment.
That's a "big step" but to me the major advantages to the Arduino are the pre-loaded bootloader and the fact that the Arduino board doubles (triples) as the programmer, the development board, and the final product/project (or as the main board in the final project). If you are not taking advantage those things, maybe you don't need an Arduino.