It seems what was initially created by God was something like “raw stuff,” Aristotelian matter without form; it was essentially chaotic, without order. It had to be given some shape or nature by God, and it did not originally have any such shape or nature. Hence, to say that the earth was “without form, and void” is to say that it was an amorphous, chaotic blob. That nicely coheres with scientific theories about the formation of the primordial earth out of a disc of dust and gas, floating formlessly in space. The early earth was deep, dark, wet (at least, full of frozen water molecules), chaotic, impenetrable mass of earth and (ice) water. That is what is meant by a “heaven and earth” that is nonetheless “without form, and void.” Then certainly “the deep” and “the waters” both might be understood as descriptions of such a chaotic and wet mass.