The figure of speech used in Gen. 1:1 in the phrase "the heavens and the earth" is called synecdoche, in which the whole is evoked by the naming of the part. "The earth" includes the earth itself, and all forms of life which live upon it. It includes the dry land and the sea, mankind plants and animals, etc. "The heavens" also encompasses all this domain contains. Since the Hebrew for "created" (BARA) is a verb in the qal form with perfective aspect, it seems unlikely that this statement refers only to the beginning of creation.
The figure of speech in Gen. 1:1 may indeed be an example of synecdoche since these two signifiers occur so often in tandem. This fact does not mean that the "heavens" of Gen. 1:1 have anything to do with the spirit realm. The heavens and the earth of Gen. 1:1 could just as well be a way of referring to the entire material order (the realm that is governed by space, time and efficient causality). The term "heavens" is apparently used this way in Ex. 20:4 and the formula "heaven and earth" in Gen. 14:22 evidently has reference to the physical universe that Jehovah produced.
As for BARA speaking about the beginning of creation, Gordon J. Wenham writes (Word Commentary on Genesis): "it looks as though [Gen. 1:2, 3] were composed by the writer responsible for v 1, and not simply borrowed from a pre-biblical source. This makes it most natural to interpret the text synchronically, i.e., v 1: first creative act; v 2: consequence of v 1; v 3: first creative word" (p. 13).
Later, he notes: "It is therefore quite feasible for a mention of an initial act of creation of the whole universe (v 1) to be followed by an account of the ordering of different parts of the universe" (Wenham 15).
With all of this in mind, I am not insisting that Gen. 1:1 simply dwells on the "beginning" and does not teach us that God finished his creative work vis-a'-vis the heavens and the earth. As you mentioned, the Qal perfect verbal stem is employed and that indicates that the writer of Genesis is depicting simple, perfective action--which means that both the inception of the creative act and its TELOS (its end) is in view. That doesn't mean, however, that the earth did not need to be prepared for habitation as recorded in 1:2. ERES in Gen. 1:1 does not seem to mean the "productive land and all that dwells therein." If we construe the verse synchronically, as Wenham and other interpreters are wont to do, then Gen. 1:2 is manifestly relating God's preparation of the already created earth.