This may be hard to explain to a non-Christian and I can understand this question because when I was an unbeliever I felt the same way but let me try to explain it how I learnt it.Why would Christ be in control of your marriage? God gave you free will.
Yes we have free will. With that free will Christians strive to make Christ the head of their lives. He is the one who designed us, the Master Architect, with a purpose. So as believers, we surrender ourselves into submission to our Creator. To HIS will for our lives because we trust Him. We trust that what He has designed for us is far greater than what we could ever manifest for ourselves.
When you have the Creator's creation all making the Creator the centre, we are more focussed on His will for us rather than our own. So, as a result, when *ish* hits the fan and the husband or the wife is not acting right, pulling their weight, doing their part, or what have you... our focus is STILL on Christ because He is perfect and just and worthy of our trust.
We humans are fallible and will fall short of what is expected of us in a relationship. God will not. Therefore if we allow Him to be at the helm of our lives this includes our relationships. He will steward us back to what is right if we keep our eyes on Him and seek to honour Him in our relationships. Even though the hierarchy is:
...everyone has their own unique and intimately personal relationship with God. So when the man (who is submissive to God) eventually falters, the woman (who is also submissive to God above her husband) can turn to God to help her get through the situation with grace, patience and love until it is made right again. Likewise when the woman stumbles and lets her husband down, the husband can turn to God for what HE needs to carry them through while the woman is also seeking Gods stewardship and guidance on how to make it right within herself.
He is the best marriage counselor there is! As we keep God the main focus and strive to be more Christ like we naturally will be better in all areas of our lives.
I hope that helps and makes sense.