1 Corinthians 14:33
For God is not the author of confusion, but of peace, as in all churches of the saints.
One flaw in man's thinking is that we so easily assume that our logic will determine truth. And while there are countless truths that can be explained logically, there is still many truths from and about God that are beyond our comprehension. These truths are no less true; and more so, it does not make them confusing because we cannot fathom them.
The verse I started with is one used many times by Jehovah's Witnesses to argue against the Trinity. They will say that the very idea of three separate persons who are all one God is confusing - and that as such it cannot come from God (who is not the author of confusion). But, it is enough for the Bible to make a claim (which is truth on the fact alone that the Bible states it).
Let me give an example; I (nor do I believe anyone) will ever, while living on earth, understand how dirt can be breathed into - and in that breath - change from dirt into flesh. To be eyes, lungs, the digestive system, a brain - in less than a moment. To ponder how and then understand that how, is beyond intellectual grasp. However, because it is said so in Scripture, I am not the least bit confused about it. It is just merely above my understanding.
And so knowing this; our very foundation of what we stand on as truth should be based from the Word of the Author of truth, God - who is the Truth. Somethings will be mysteries, and maybe in eternity (a mystery in itself) all will be understood; maybe not.
I imagine that a line cannot fathom a sphere. And we being within the line of time, have no idea what complexity (or simplicity) there is in the realm of eternity. God sees all, knows all, is in control of all; yet He works in the present, He even allows the future to be shaped by our decisions and actions. Should this limit our faith, when we don't understand something? I say it should cause us all the more to give all our faith to Him; who is God, Jesus Christ.
1 Timothy 3:16
And without controversy great is the mystery of godliness: God was manifest in the flesh...