Ok, let's get started.
Things you need:
GUI Studio MDL (http://www.wunderboy.org/apps/guistudiomdl2.php
Maya plugins for Import/Export SMD (https://developer.valvesoftware.com/wiki/Maya
I do not use Maya myself, I am using 3DS Max 2012 but I think it should be the same process.
Anyhow, first off: You need to open the MDLDecompiler and find your model that you want to decompile so that you can open it up in Maya.
When you've found the file, pick an output folder and click Extract.
When this is done, you will get a couple of files in your output folder. Alot of .SMD files (which are the models-files) and a .qc file.
Now you start up Maya, hopefully you've found a couple of plugins which will let you to import .smd into Maya. Edit the things you want to do and then export them, preferrably with the same name, unless you want to go into the .qc file and change unnecessary stuff. (This is a basic tutorial after all so, I won't go into that :P).
(Actually, from this point on, it's better if you're following Nahka's tutorial, he's far better than me to explain stuff)
Now it's time to start up GUI Studio MDL, it needs some cofiguration the first time you start it up, but if you go and read up on Nahka's pony compiling tutorial it should be a pretty good explaination how to do it there.
When you're all set, load the .qc file which you extracted before and press Compile.
If you have the same "Target Mod" as stated in Nahka's tutorial, it will be in
C:\Program Files (x86)\Steam\steamapps\-Your Steam Name-\half-life 2 episode two\ep2\models
It's usually here that things really shits themselves, compiling errors yada-yada-yada. If this happens you usually need to go in and change stuff in the .qc file, which you open with ze Notepad++. But some of the most common problems are listed in Nahka
's tutorial so check it out or ask here!
If everything works out, you should have a new set of MDL-files somewhere in the path listed above, you can check the .qc for the exact path.
Just take these files and put them where you found and decompiled the original model and you're set.
This will overwrite the original model though ,so be sure to keep a safe copy.
So good luck :)!