How is Acts 7:48 reconciled with omnipresence doctrines? Some verses seem to indicate that God is indeed not omnipresent such as Acts 7:48, "The Most High dwelleth not in temples made with hands". How is this specific verse reconciled with the doctrine that God is omnipresent?
'Dwelling' does not simply mean to 'be present'. It means to reside or inhabit. If you go into a shop, you are not 'dwelling' in the shop, but you are present there. If you say "I do not dwell in the shop" it doesn't mean you never go in there, or that you are not there now.

The point is that God is above 'dwelling' in places that humans have made. He has his own 'dwelling places (in so far as he dwells anywhere), but has no need of human temples.