Download and unpack all files to your main Amnesia folder, and merge when prompted.
Make sure that resources.cfg and DevIL.dll go in your main Amnesia folder, and that the Simulacrum folder goes in \custom_stories\
DevIL.dll is required for users running Amnesia 1.3.1 to render skyboxes properly.
The custom resources.cfg is optional but recommended in order to use the custom spotlight lantern. It is advised to make a backup of your original resources.cfg before doing so.
for GOG.com users:
Unzip Simulacrum.zip to C:\Program Files (x86)\GalaxyClient\Games\Amnesia - The Dark Descent\
C:\GOG Games\Amnesia - The Dark Descent\
for Steam users:
Unzip Simulacrum.zip to C:\Program Files (x86)\Steam\steamapps\common\Amnesia The Dark Descent\
It is highly recommended to play with Stayd's Enhanced Shaders for Amnesia.