Use /firstScoreAbs true command option (Tested in version 4.7.2):
If this option is set, the score reported by the engine is taken to be
that in favor of white, even when the engine plays black.
"stockfish_4_32bit.exe" -fd "path\Stockfish" -fUCI /firstScoreAbs true
xboard is not a UCI user interface, so you'll need to install the Polyglot adapter to make it work. Once you have the Polyglot installed, you'll need to edit the polyglot.ini file. Read here for instructions on how to do it.
Please note Polyglot is not a very professionally made software. You'll only be able to find some old documentation. The whole process ...