I'm the developer of LaTeXTools. To set the master file, you need to add the following line at the very top (i.e. as the first line) of any included files:
%!TEX root = yourmasterfile.tex
The README has further details.
Right now there is no support for setting a compilation directory other than the one where the master file resides. It's something a few users have requested, so I may get to it eventually, but it will require some pretty extensive changes (I think).
Update: If you're using a .sublime-project file, you can add the master file under the settings property. See the official README.
In my case I had to provide the absolute path for the