Changing some prefrence.txt and settings

Two basic questions.

  1. Can I change the location of preference .txt
  2. I want to use timer0 ISR in my code. how can it be done without modifying the basic structure of Arduino.
  1. Can I change the location of preference.txt

No, but many of the settings can be overridden in boards.txt

  1. I want to use timer0 ISR in my code. how can it be done without modifying the basic structure of Arduino.

As long as you (and any libraries you use) don't need the Arduino time functions (millis(), delay(), micros()) you should be able to take over the Timer0 ISR. If you use the Arduino timer functions you should pick a different timer. Why do you want to use Timer0?

John thanks for the reply.

in my present case I am not using any of the library functions which are based on timer0. but in some other project i might need those functions so don't wish to disturb the system files of Arduino. this moment I made changes in wiring.c (disabling ISR there) so it wont give me error. but then is there any way i can use my own ISR without actually making changes in system file. In current project i need three timers doing all the jobs interdependently. I like to use arduino in my project. but not at each place. we need to understand it and optimize our code for effeciency. I believe Arduino is a great tool that brings down your development time.

well for example.
if i need high speed PWM with necessary frequeny. I would change the required registers. would define a small function to disable pwm.
something like
#define setPWM1 (TCCR1A = TCCR1A | B10000000)
#define clrPWM1 (TCCR1A = TCCR1A & B01111111)
#define setPWM2 (TCCR1A = TCCR1A | B00100000)
#define clrPWM2 (TCCR1A = TCCR1A & B11011111)

but to initialize i would use analogWrite function. that would save my other efforts.
after proper initialization is done I would just refresh the values of the PWM registers without using analogwrite() to refresh the values of PWM, making the whole thing fast.

But then the same could be true about the timers. and for this reason I am trying to find a way that i can use my ISR without making any changes in system files of arduino.