Tree hash and multithreading for parallelism I am using tree hash mode of Skein on a 16 core processor. Will it automatically employ parallelism using more than one cores or do I have to use multi-threading within the tree hash for parallel processing?

Also, the tree hash mode requires three parameters: leaf size encoding, fan-out encoding and tree height. Except for the last one, I am confused about the other two parameters, what are they exactly?
On multi-threading: Read the code.  As Paulo writes, that's up to the implementation.  Read the source code of your library and see for yourself what it is doing; it shouldn't be too hard to figure it out.