MSU patches are processed using the Windows Update Stand-along Installer (wusa.exe) The Windows Update Stand-alone Installer uses the Windows Update Agent API to install update packages. Information about this process can be located here.
As an example: LANDesk Patch Manager would install this update by running the following command line:
WUSA.EXE windows8-rt-kb2871690-v2-x64.msu /QUIET /NORESTART
Similarly you could set up a script or package to run the same commands to install the patch or other .MSU package.