So in your mod folder would be a mod.ff ,mod.iwd. In your mod folder and inside the folder you named for your new mod would include the mod.iwd and the mod.ff thats included with the mod and all server configs needed to start your mod. Your server should have a cod4 folder and inside that a mods folder and inside that a folder named the name of your mod or ect. For mods say you are using Extreme X4 2.0 for instance it doesnt matter which mod most all mods would be installed the same way as Extreme X4 2.0