Mugbill is right. You can have a "mods" folder in the SOMA root and the launcher will look for mods there. I'm putting together a little text for setting up mod entries, should be up soon, but as a quickstart guide:
If you are creating a custom story, save it under the mods folder, name it whatever you want (mods/mymod). Then, inside 'mymod', create an entry.hpc file, with the following contents:
<Content
Author="Me"
InitCfg="config/main_init.cfg"
Type="StandAlone"
Title="MyMod"
Description="This is my mod"
/>
Then, have a 'main_init.cfg' file located in 'mymod/config' containing the following
<Directories
MainSaveFolder = "MyMod"
BaseLanguageFolder = "config/"
GameLanguageFolder = "config/lang_main/"
/>
<Variables
GameName = "MyMod"
/>
<StartMap
File = "level1.hpm"
Folder = "maps/"
Pos = "PlayerStartArea_1"
/>
So this would tell the game to start the "level1.hpm" map, and this file should be placed under a 'maps' folder, best if located in its own folder as well, this means in 'mymod/maps/level1'.
Finally, a resources.cfg file in the mod root folder, looking like this:
<Resources>
<Directory Path="/maps" AddSubDirs="true"/>
</Resources>
And after this you should be able to run the mod through the launcher. Keep in mind that this guide is superquick and that there are lots of stuff that can be changed, but this should work for running custom maps.