1. Make a folder (in C:\Program Files (x86)\Amnesia The Dark Descent\redist\custom stories) with the name of your Custom Story. If you don't have a name for your CS, that's okay. Just call the folder "MyCS" (I'll refer to this folder as MyCS from now on). You can re-name it later if you'd like.
   
2. Add another folder inside MyCS titled "maps" (without the quotes) and drag your maps (along with any script files) in to this folder. Note: You cannot save new maps directly into this folder. Save them to the desktop, then drag them in.
   
3. Create a new text file (with Notepad++ or Geany preferably). You're going to need something like this in it:
   
   Code:

   <Main
    Name="MyCS"
    Author="Me"
    ImgFile="example.jpg" //can leave this blank (just "") for no image

    MapsFolder = "maps/"
    StartMap="startingmap.map"
    StartPos="PlayerStartArea_1"
/>
   Replace the text as needed, then save it as a .cfg (a configuration file)
   
4. Place this new cfg file in MyCS (not in maps)
   
5. You can also include a .lang file, titled "extra_english"
   
   Code:

   <LANGUAGE>
    <CATEGORY Name="CustomStoryMain">
        <Entry Name="Description">
        Type a description here (use [br] to skip a line)
        </Entry>
    </CATEGORY>
    
    <CATEGORY Name="Inventory"></CATEGORY>

    <CATEGORY Name="Journal"></CATEGORY>

    <CATEGORY Name="Levels">
        <Entry Name="Next Map">Next Map's Name</Entry>
    </CATEGORY>

    <CATEGORY Name="Hints">
        <Entry Name="Broken Door">This door won't budge</Entry>
    </CATEGORY>

    <CATEGORY Name="LoadingText"></CATEGORY>
    
    <CATEGORY Name="Signs"></CATEGORY>

    <CATEGORY Name="Ending">
        <Entry Name="MainCredits">Thanks for Playing!</Entry>
    </CATEGORY>
</LANGUAGE>

Anyways, that's all I can think of. You'll want to test lots and lots and lots. Test early, test often, and listen to constructive criticism ;)

Some Useful Links
A list of engine script functions
Your Computer's tutorials
Screenshot Criticism Thread

A note about the screenshot thread:
There's *ALWAYS* room for improvement in mapping, no matter how good you are, there's always something you can do better. If you don't feel comfortable posting a screenshot there, just take a look at the advice other people are given - learn from their experiences too!