CrossRoad you are great
Thank you for you quick replay
But as you probobbly thought.....I have few more questions 
Iused to work with AVR (i.e. Atmega32 )and burned them with the ISP MKII.
Never used a Bootloader but every time Iplayed with the fuses something went wrong and I had to burn them in High votage using the STK500 or some thing like that !
So I am very scared when I hear the word Fuses!!
- If I would brn the Bootloader would I be able to run it over if something went wrog?
- Can I try to burn Bootloader on my ATmega2560 arduino Board- would it damage the USB port (I wont be able to load program via the USB?)
- Should I burn the Bootloader that is in the arduino compiler
- How can I burn the Bootloader - is it aregular Hexfile that I can load using the studio ?
- If I burn the Bootloader, and then burn a sketch (lets say the blink one) wouldnt it run over the bootloader?
- why am I asking too much questions.....because I built aPCB and put about 3000$ on assmbley and design and I am so scared to damadge it and I have a very rough dead line
Thank you again for your help