> I want to know how to program the atmega328 with pro mini. I don't want to use external crystal for my projects.
See "Minimal Circuit (Eliminating the External Clock)" in : http://arduino.cc/en/Tutorial/ArduinoToBreadboard
> I have seeing examples with other arduino boards, to use arduino as ISP. is it possible with pro mini board.
Yes. Use pins 10, 11, 12, and 13; just like on the Arduino UNO.
> After flashing the intial bootloader in my mega328, will it possible for me to directly download the code from arduino IDE, if i create a seperate hw.
Yes. You will need the same USB-to-Serial cable you use for the Pro Mini.