I went through the following tutorials in the last few days. The project is still forked from the last year's repository. I will call this copy as v1.0 aka the starting point of my project.
Here is some good information of .nwk files.
Please don't overlook the See Also and References on the bottom of the page. They also have pretty good material. There is also an example of a large phylogram with its Newick format representation.
As far as the kml is concerned. Here is what I went through. The kml is actually quite easy to learn. Now I have to focus on how can JAK be used to create kml's with the various kind of rich features that kml supports