I am going to answer my own question.
I sit down, and took an hour or two to read through every plugins' documentation.
My conclusion is that - for those parameters that has to be tweaked, they are very easy to understand and well documented. For those complicated matter, the default are most like fine.
The craft sequences are stored in skeinforge_tools/craft_sequences/ file. It's a good place to start with and follow the documentation of every tool from top to bottom.
I need to make a few edits to change M104, M108 output from Sxxx to Pxxx though, so that the Linux EMC2 would understand.