The classic Christian and Jewish concept of God includes his omnipresence. God is nowhere in particular and, in a sense he is everywhere at the same time. David asked rhetorically about God in Psalm 139:7, Where can I go from the Lord’s presence? The presumed answer is that God is omnipresent. There is nowhere we can go and God is not there.
Yet, there is a limited number of times in both the Old and the New Testament in which God appeared to a human in a visible or audible form. This appearance to humans through their senses is called theopany. God appeared as a flame in a bush to Moses. He appeared as a “still small voice” to Elijah. He spoke to Jesus and to Peter, James and John on the Mountain of Transfiguration. There are several other theophany moments in the Bible.
I am not exactly sure what your question is, but perhaps it is how can God be everywhere equally, yet at the same time appear in a particular place? My answer is that I suppose God can do whatever he likes to do. If he wants to appear to an individual in order to communicate with him or her, God can choose to do this, but if he does, then it will be a theophany, in which case God appears to be in a particular place. The key word here is appears. In order for God to appear at all, then, by definition, it has to be in a particular place and time. I suppose some might say that if God is omnipresent then he must be equally everywhere all the time. But this is an assumption and it is apparently not true of God, given the biblical witness. God is everywhere all the time, but it is apparent that the actual God who exists has the ability to make a physical or auditory appearance of himself if he so chooses. Who decides that God cannot do this? Does the word omnipotent define what God can or cannot do? There is no logical requirement that a being who exists everywhere cannot also exist simultaneously in one particular place, We could define omnipresence this way, but defining something does not make it true.
This may make a philosophical problem for you, and I can see why, but, apparently, it does not create a philosophical problem for the God of the Bible.
As for the incarnation, this is a clear example of theophany when “the Word became flesh.” If I understand it correctly, Jesus chose to limit himself when he incarnated. His omniscience and his omnipresence were somehow limited when he came in the flesh. Again, if this appears hard to accept, what matters is that it is true. While in the flesh, Jesus did not know the time of his return (Matthew 25). He knew a woman touched him, but he did not know right away who had touched him. Jesus allowed his deity to be limited when he was incarnated. If this causes a philosophical problem for one of us, it is still, nevertheless, true. We do not get to define who or what God is, and our philosophical categories do not define who he is as well.
I hope this helps.