Whenever God is referred to in physical terms it is meant as a metaphor. It is axiomatic that God is not physical and has no physical properties. We, however, are physical and can only understand things from a physical frame of reference. Therefore, the use of the physical is a helpful metaphor for the understanding of the qualities of God.
What is the metaphor of referring to God as “HaMakom”, meaning "The Place"? If you think about the meaning of a "place" you'll agree that it is more than just a geographical location, it's a space which is capable of containing something else. When used in reference to God it means that everything is contained within God (conceptually), whereas He is not contained in anything. As our Sages teach, "He [God] doesn't have a place; rather He is The Place of the Universe."