Here is how I believe spells work...
I believe that the Universe vibrates with an energy that is in and all around us. We are all connected through this energy. I personify this energy into various gods and goddesses to help me to better connect to this energy (I am a pantheist). Not only does the Universe itself vibrate with energy, but so does everything within it... black holes, galaxies, stars, planets, rock and stone, even gases, living things (including bacteria, plants, animals, intelligent life...), and even the smallest grain of sand and the atom and all it contains. Everything vibrates with an energy.
Many things in nature carry specific energies that our ancestors (the ancient pagans and indigenous spiritual folk) observed. When we do a spell, we are combining energies (of our tools- which we've infused with specific energies, of the herbs, stones, colours, elements, our own energies, and the pervasive energy of the Universe), raising that energy to a climax, then directing that potential energy and making it kinetic... sending it out with our intent.