"How do you explain how He entered the Upper Room?"
He can walk though walls - but he can't be in two rooms at once - that would be a denial of the reality of the incarnation.
First, there is a bit of a confusion here. The Real Presence in the Eucharist is resurrected Christ, not incarnate Christ. That is the Christ entering the upper room.
However, your apparent insistence that incarnate Christ be denied His divine nature, which includes omnipresence, is, I believe, Arianism, if I can keep my heretics straight. Is walking on water denial of the reality of the incarnation?