Now I haven't figures this all yet but I though about having anything living in my universe have a soul and the universe itself. Basically each soul is linked to something like the universe, a planet, a person etc. and each souls are "particles" of the soul above it in the hierarchy. So the 10 or so gods of my world would only be parts of the greater soul of the planet etc.

The trick is that as you go deeper and deeper the power of the soul is weaker and you end up with mortal creatures at the end. Now this whole organization wouldn't exactly be known to the people of the world but it's something I set up for it. The mortals would just think of gods in the ways you'd expect but this leaves the possibility of different religions which I find more hard to explain in a world where gods can just manifest themselves precisely as a specific being.