can some one explain maybe in short, what is actually going on, bootloading arduinos?
The 2 USBs are for 2 interfaces into the memory area.
When you install the bootloader via the ISP interface, the Flash area is being accessed pretty directly by the programmer. Same for File:Upload Using Programmer, when a sketch is loaded and the bootloader is wiped out; the Flash is accessed by the programmer.
When you install sketch via the serial interface, the bootloader is running as a sketch and receiving the data and putting it into Flash.
There is way more detail you can read about in the '328P datasheet, Section 27 and 28.