Designing is an act of meditation. To truly design a space that works with nature and integrates all the elements in harmony you must be in that space and imagine what it would be like if you placed a wall here or a patio there. To visualize a structure and its' relation to the natural environment of the site you must go there, walk the site, sit and sketch your ideas as they come to you. The best way to do this is to be there before the sun rises so you can see the changing colors of light from the first rays through mid day to the setting sun. You can't capture the small nuances of the topography of the land sitting in an office fare away from the site.
The first consideration when designing a sustainable dwelling is the size of the physical foot print of the structure. We must endeavor to tread softly on nature, building structures not on top of nature with walls that lock out the natural world, encapsulating us in hermetically sealed boxes but instead we must build structures which embrace nature, which integrate and emphasize a site's natural features. Minimizing the physical foot print (the space in terms of square footage that the structure will take up on the site) can be achieved in many ways. Part of the structure can be place under the ground or alternatively you can cantilever spaces out over open ground leaving a relatively large amount of the site to nature.