[Lazy_Perfectionist]

Part One
From main menu
Preferences->Mod preferences->click on name to enable.

The game will remember which mods an existing game was created with. Before you start, you need to make sure proper mods are enabled. After starting, it will automatically apply the correct mods every time you continue that existing game.

If they have a bunch of extra files, then they go in the mod folder as well. Just be sure to preserve the zip files directory structure in that case.

E.G. Mod alpha is distributed as a zip file. You open up the zip file and you discover a readme file, alpha.dm, and a folder called alpha. You unzip the entire thing to your game directory. in the end it will look something like this:
Dominions 3\mods\alpha.dm (mod file)
Dominions 3\mods\alpha.tga (mod icon)
Dominions 3\mods\alpha\1.tga
Dominions 3\mods\alhpa\2.tga
etc.