Given the importance of natural resources in both Economic Geography and Ecological Economics I also wondered what the relationship was between these two in particular.
I see both Economic Geography and Ecological Economics as different.
Economic Geography is the study of the determinants and effects of the spatial distribution of economic activity. Economic Geography is considered as a sub-field of economics, so it's applying standard economic thinking to the geography. In particular, Paul Krugman studied the location of economic activity across space, using agglomeration economies to explain why industries cluster within particular countries and regions.
According to Robert Costanza, Ecological Economics is a transdisciplinary field. It studies the interdependence and coevolution of human economies and natural ecosystems. It's true that this coevolution is studied both intertemporally and ... spatially, but not as a sub-field of economics. It's an attempt to look at humans embedded in their ecological life-support system, not separate from the environment.