One of the more difficult things about morality is that, because of sin, even the clearest statements in the Bible become difficult to follow. Take, for example, the command to honour thy mother and father. This seems fairly easy, right? This may be so in a natural family. But not every family is in its natural state. Do we honour step parents as well?
As it happens, this is a question Jesus Himself had to answer. Though Mary was His natural mother, Joseph was His father only through his marriage to her. Joseph was Jesus' step dad. And yet, not once do we hear of Jesus giving him any trouble. None of this "you're not my real dad!" nonsense. Jesus honoured and obeyed Joseph as would be appropriate for Him to treat the paternal head of the family if He was a normal human being living with His natural parents.
With Jesus' perfect example, we see that even in a sinful world, God has given us everything we need to obey Him. Commands that apply to, or are written for the ideal scenario can still be applied to less than ideal scenarios (not that there was anything less than ideal about Jesus' family situation). We can take any command in scripture and apply it faithfully to the situation in which we find ourselves. As honour thy parents applies to step parents, too, so also do God's other commands cover more than just the specific scenario they were written for. It takes wisdom, but a faithful and prayerful study of the scriptures will fully equip us for everything we need to do.