You need both. Files from V1.3.1_V1.3.2_Upgrade should overwrite those from mb2-v1-3-1.
So you put MBII folder of mb2-v1-3-1 to ~/Library/Application Support/Jedi Academy as @kikili wrote, then move files out V1.3.1_V1.3.2_Upgrade to ~/Library/Application Support/Jedi Academy/MBII, click "yes"...