If you are really asking how to use it then just look at the documentation that comes with it. If there is some part you don't understand then post it here.
If you do mean how it actually works, I'll give a brief explanation here.
1) When you open up SCMLoader.exe, it calls a function in SCMLoader.qdp (really just a .dll file) -- SCMLoader.qdp is the real program, the .exe file is just a small program for starting it up, since DLLs cannot be run directly by clicking on them.
2) After having been loaded by SCMLoader.exe, SCMLoader.qdp loads Starcraft in a suspended state so that it can perform patches to it.
3) At this point it uses a technique to load itself into Starcraft's process space and then Starcraft is allowed to resume.
4) When loaded into Starcraft's process space, SCMLoader gets control before Starcraft does and starts its own initialization. During this it checks the Starcraft version so it can possibly find a match to a set of graphics loading/unloading function addresses from its list of ones from various Starcraft versions. Some Storm.dll functions are also set to be hooked by SCMLoader during this initialization so that it can intercept calls to those functions.
At this point the initialization is complete. The primary functions that are hooked are SFileOpenArchive and SFileOpenFileEx. When SFileOpenArchive is called, SCMLoader does something like this:
1) If the archive ends in .scm or .scx, continue with some additional processing; otherwise just call the real SFileOpenArchive.
2) Perform any cleanup needed from the previous scm/scx.
3) Call SFileOpenArchive for giving the handle that Starcraft expects, but give the scm/scx significantly boosted priority when calling it.
4) Open an additional handle to the scm/scx with 1 less priority that will be kept open until another map is loaded, since Starcraft doesn't keep the scm/scx open while loading certain data files.
5) Check for modded graphics and if they exist then call the functions in Starcraft for reloading the graphics.
6) Check for a file for a playlist in the scm/scx (in the format for my playlist plugin).
7) Open any MPQ packs referenced by a certain text file in the scm/scx, if it exists.
SFileOpenFileEx is hooked so that SCMLoader can be signalled for other various events which I won't be explaining here right now.
-EDIT-
Heh, I guess you just meant how to use it. I had typed up all of that before reloading this to see if you had replied again yet. Oh well, some people probably were curious about how it works anyway.
To add mods to the map, just add them to the scm/scx exactly like you would if you were adding them to an mpq archive. Then to play the mod, run SCMLoader and play the map that you added the mods to.