I'm not familiar with that tool, so I don't have an answer for your specific question. But here are two pieces of advice:
1) there are many arduino simulators that you can use to single-step thru the code.
2) The Arduino is small and simple enough that you should be able to reverse engineer it using only the (dis)assembly and your brain. (Unlike the x86, ...
The .org-directive set's the location counter, so essentially what they do here is telling the assembler that this code should be placed at 0x00 of the current section, which happens to be global 0x00 aswell and that address seems to be executed on reset on this particular CPU with this particular configuration.