Nah, it's no problem
- Go to your Amnesia install directory. If you're using a retail copy, this is the "redist" folder, and if you are on Steam, then it is the "Amnesia - The Dark Descent" folder.
- Scroll down to a file called resources.cfg and open that up with a text editor, such as Notepad.
- At the end of the file, but before the </RESOURCES> tag, add the contents of the code block I posted above there. This will tell Amnesia to start looking in the custom_stories folder for resources.
If the CS still doesn't appear in Amnesia's menu, can you post the contents of your custom_story_settings.cfg ? If there is anything wrong, it must be that, unless you don't have a map for your custom story