There is nothing to reconcile, and I will illustrate it in two manners.
God the Almighty
Christians believe that God is transcendent. He is not bound the universe. He is not described by physics. The uncertainties described by quantum physics are no different.
You have already recognized Christianity recognized God as Almighty. Even if we gloss over that whole creatio ex nihilo thing and stick to just to a couple of Christ's miracles, we see that Christians already believe that God is not bound by the laws of physics.
Feeding of the 5000
One of His disciples, Andrew, Simon Peter’s brother, said to Him, "There is a lad here who has five barley loaves and two small fish, but what are they among so many?" Then Jesus said, “Make the people sit down.” Now there was much grass in the place. So the men sat down, in number about five thousand. And Jesus took the loaves, and when He had given thanks He distributed them to the disciples, and the disciples to those sitting down; and likewise of the fish, as much as they wanted. So when they were filled, He said to His disciples, "Gather up the fragments that remain, so that nothing is lost." Therefore they gathered them up, and filled twelve baskets with the fragments of the five barley loaves which were left over by those who had eaten. [John 6:1-14 NKJV]
How is that to be understood under the laws of physics? Start with two small fish and five loaves of bread. Feed 5000 people and still end up with twelve baskets of bread. Conserving matter and energy does seem to limit God.
Walking on Water
After feeding the 5000, what does Christ do for an encore? Walk on water:
Therefore when Jesus perceived that they were about to come and take Him by force to make Him king, He departed again to the mountain by Himself alone.
Now when evening came, His disciples went down to the sea, 17 got into the boat, and went over the sea toward Capernaum. And it was already dark, and Jesus had not come to them. Then the sea arose because a great wind was blowing. 19 So when they had rowed about three or four miles, they saw Jesus walking on the sea and drawing near the boat; and they were afraid. But He said to them, 'It is I; do not be afraid.' Then they willingly received Him into the boat, and immediately the boat was at the land where they were going. [John 6:16-21 NKJV]
Again, this is completely unacceptable to physics. For the sake of argument, let's say that God isn't required to obey the law of gravity. We could write a book full of the miracles of God (I think maybe that may have already been done), all illustrating that God is not bound be the laws of physics.
Physics is limited
In asking how can God know position and momentum at the same time, you have made a categorical error. Physics, like all science, is limited to describing what can be observed. Physics has no basis for observing the way God's knowledge works. Assuming that God must make observations, that He must interact with creation is without basis. Attempting to predict the outcome of God's actions, God's knowledge using physics is logically flawed. You can not draw a conclusion without first satisfying the premises.
Addressing a comment
Probably, but the bits we know, we know. And to all intents and purposes [even if just to play Devil's advocate] you should accept that things don't have definite position or velocities. How does that work with Omniscience however is my question
Again, there is nothing to reconcile. If things don't have definite position or momentum, then not knowing a definite position or momentum is not a challenge to omniscience. If you like, you can just assume that God groks the full evolution of the universe in whatever physical model you like.