Bootloading Atmega328p-pu with USBTiny AVR Pocket Programmer

Thanks,
ll have to look up section 27-28, but I still dont understand, why Im not simply programming the bootloader. Its only a little programm, executing instruction after instruction. I also wonder why this proramm is nowhere to be found, its got to be a .hex file. Ok, there are different ones for different controllers. As far as my understanding on µcontrollers goes, the 328 must receive and give commands over its serial interface through its usb from the Ardu sw, to and through the programmers usb to the programmer, which not only talks back and forth to the Ardu sw, but also flashes the 328s memory with data from the bootloader.hex. So 2 usbs communicating, and the 328 communicates with Ardu sw while being programmed, with data comming from Ardu sw.
Maybe Ardu sw is telling the prorammer where the boot.hex is?
I found out about how to install the bootloader from this source: http://itp.nyu.edu/physcomp/Tutorials/ArduinoBreadboard
Is there any Arduino publication about it? I mean this is so far out, ... I`ve never even heard of anything like it, if someone would have told me, I would not have believed it.
Very complicated.
Thanks anyway

John