A couple of limitations to consider:
How much time do you have in your story to achieve the enhancement desired?
If you are not in a hurry, a good plan is to imitate Nature, and make very small modifications over many generations. This provides large room for error by allowing natural selection to do its job. If the modification is a good one, then it will survive the test of time and continue to appear repeatedly. When satisfied with the results, another very small modification is attempted.
How much are you willing to risk your one cell that is being modified?
Considering how often unexpected genetic mutations are rejected biologically through spontaneous abortion, there is a high rate of rejection to certain gene modifications that are not compatible with life. Making modifications at a one-cell level for what becomes a many-celled being then, seems to take a bit of finesse, even assuming full knowledge of the genome and using advanced technology. If you are willing to accept very high risk to this one cell that, left alone, has a fairly good chance to survive, then you could try at that level. This could be because although you know the genome well, you don't yet know how changing that genome will affect how it materializes physically.
If you are not willing to risk that life, then waiting until it is fully mature and able to consent to providing unpaired sex cells (egg or sperm) for modification prior to forming the whole next being is a more prudent route.