Here's more on the meaning of HaMaKom:
Whenever G-d is referred to in physical terms it is meant as a metaphor. It is axiomatic that G-d is not physical and has no physical properties. We, however, are physical and can only understand things from a physical frame of reference. Hence the use of the physical as a helpful metaphor for the understanding of a quality of G-d.
What is the metaphor of HaMakom ("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 G-d what it means is that everything is contained within G-d (conceptually), while He is not contained in anything. As our Sages say: "He [G-d] doesn't have a place, rather He is The Place of the Universe."
The above is from Ask the Rabbi in a letter to a man named Jasper.