Not to sound like shamless plugging, but you can look at how I do it for my mod at:
http://forums.demigodthegame.com/369526
Pretty much, you create a mod folder that goes into the Demigod's mod folder that stores all of your files in the correct directory structure. Mine has these files:
bindata\mods\Rollover Mana and Equipment Display\mod_info.lua
bindata\mods\Rollover Mana and Equipment Display\hook\lua\ui\game\HUD_rollover.lua
The mod_info.lua is needed by the Mod Manager.
The hook folder pretty much tells the game to overwrites the default files with your own (although it isn't a total replace, it is more like an add-but-replace-all-of-the-functions-with-the-same-name) =P (I could be wrong though; I am more of a pick-up modder)
HUD_rollover.lua is the file located in dgdata.zip that I edited that shares the same path.
Oh, and the mods do not take effect until the game has started in a match, so no mods will work that change the lobby, intro screen, or anything like that.
Oh, and there are two different types of mods for this system. UI mods and gameplay mods. Gameplay mods require everyone in the game to have them activated, while UI mods do not, since they only change the UI and none of the real gameplay data. If you want to make sure that you specify in your mod_info.lua which type yours is.
Feel free to ask any more questions. I'll try to answer as best that I can. My experience is from making random, silly mods in Supreme Commander (and some in Demigod since the betas), and I have done a lot of "different" things with this engine, so I should hopefully have some insight into what you want to do. Plus there are a lot of others that are quite knowledgeable about this stuff around here as well =D
