When Dr Joe refers to space, he is referring to the space that exists between everything and all around us.
In addition, when Dr Joe mentions to "be aware of the space between your ears, in space" (for example), he is asking you to be aware of the space that exists between your ears while maintaining a sense of being in space or the quantum field.
The Quantum Field: A field of information beyond this realm. In this quantum realm, a realm that exists beyond space and time, there is no separation and everything material is interconnected in oneness.
For more details about Meditation and Dr Joe's use of Space, we recommend watching the video above where he explains it in detail and reading Dr Joe's books Breaking The Habit of Being Yourself and/or You Are the Placebo.