Launch the game. If your directory looks more like mine, mods should work. Best indicator is that a console window pops up in addition to the regular game window. Ingame you can press F5 to en-/disable mods and configure them.what do i do next?
Btw, if this is your first time playing, it's highly recommended not to play Complex Breeding, as that mod disables all tutorials and dialogues.
If it still doesn't work, I'd recommending deleting your game folder, then starting over by following flannan's
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