Here is a book
that addresses your concern. It's been awhile since I read, but if I recall the solution is the following:
Once a species of hominid had evolved up to the point of being fit matter for the infusion of the rational soul, God infused a rational soul into the zygote of one of these hominids in utero, thus changing it into a human being. He interprets Eve being created from Adam's rib, as a second zygote splitting from the first. So Eve comes from the "side" of Adam when she was twinned. But it is a special case of twinning since they were obviously not identical twins. Eve had to be given two X chromosomes in this process. But the author says this is no more strange than the Blessed Virgin conceiving by the Holy Ghost.
I thought it was a pretty clever explanation myself. He doesn't speculate on what happens after this, but you there are quite a few ways of filling in the story. The hard part is dealing with the act of creation. Of course all of this is nothing more than conjecture attempting to fill in the gaps left by what we know for certain from revelation.
You can read the book and see for yourself. It might give you some peace of mind. After I read it I realized that after all of the elaborate hypotheses you still end up with "God did it". I would follow the advice of the desert father someone quoted earlier.
That's pretty neat, but it still doesn't resolve the question of Adam and Eve being raised by non-human hominids and Eden having ape men bounding about in it with no mention of these ape-men or Neanderthals in scripture. Yet we have fossils for them and know they existed. It is completely confusing.
We know Eden was in Mesopotamia, or present day Iraq. Perhaps modern rational man was created from mud there, but archeologists have the earliest skeletons of the homo sapien species in Africa.
I just don't see how the two stories reconcile. You'd have to take a REALLY liberal reading of Genesis or else ignore the fossil record.