It take consciousness to be emanating from particles the size of atoms. They word those atomic particles as 'atma' ( in english souls, some even call it spiriton!).Those particles are fundamental to the universe and indivisible like quarks, bosons etc. Like radiation emanating from sun, it handles consciousness as 'emanating' from soul.
Each and every living being starting from size of a cell has a soul feeling (partially) about mechanisms of its body. A multi-cellular organism is then explained as a universe in itself where millions of cells with souls are thriving. The organism will then contain a 'chief soul' directing the working of whole body (which will be us case of humans). Further the philosophy expands this concept to the real universe in which all organisms with their individual consciousness are directed by a chief 'super consciousness'( in Vedic terminology it is termed as paramatma, some translate that as equal to God Concept) Although then it further expands by saying that there are infinite (almost) parallel universes but that's other thing...