In your main Amnesia directory (where you dropped your editor files) there should be a folder called
custom_stories
In there, create a folder so that it's the name of your story.
In that folder, you'll need at least one folder and two files.
Create a folder and call it maps, and then drag and drop your map into that folder. Peace of cake.
Next, you'll want to create two text documents.
Create a custom_story_settings.cfg file. Be sure to alter the extension to .cfg so it's not a .txt.
I've taken the liberty of showing you what you'll need in there.
<Main
Name = "[Name of your custom story]"
Author = "[Your name!]"
ImgFile = "[Can leave this blank if you wish]"
MapsFolder = "maps"
StartMap = "[Mapname as well as the .map extension. eg. Intro.map]"
StartPos = "[Name of the PlayerStartArea you have in your map.]"
/>
Next up you'll want an extra.lang file. It varies depending upon your language, but I'm going to use english as an example.
So, again, create a new text file and call it extra_english.lang. Remember to alter the extension to .lang.
<LANGUAGE>
<CATEGORY Name="CustomStoryMain">
<Entry Name="Description">[The description of your custom story]</Entry>
</CATEGORY>
</LANGUAGE>
Sometimes the engine requires a resources tag in there. This is easy enough to add. Just add
<RESOURCES>
</RESOURCES>
before or after what I posted. If you have further questions, feel free to ask me.