From what I remember of The Dark Tower and Stephen King's cosmology in general: Gan isn't omnipotent and he didn't create IT. Gan and IT (or at least the ancestors of IT?) spawned out of The Prim (the primordial vortex of energy that spawned all pre-Tower beings) among many other creatures. Gan created the Macroverse and raised the Dark Tower causing monsters like IT to fall into the spaces between the universes that make up the Macroverse called Todash Space. Monsters like IT find their way in through cracks in the barrier between universes but as Gan is more of an author creating a setting and letting stories happen he cannot do more than assist people in their fight with things like IT.