The way I understand it (and I am neither a theologian nor a cleric):
God is, indeed, omnipresent. It means that He is simultaneously everywhere, not bound by any spacial limits. You cannot imagine a smallest point (like a trace from the touch of an ultramicroscopically thin pencil, or something - smaller than a bacterium, smaller than a virus, smaller than an atom, smaller than an elementary particle) - where God would not be. On the other hand, you cannot imagine the vastest space, the most colossal number of galaxies and supergalaxies scattered over millions or billions of light years where God would not be covering all. He is, in His fullness, in the smallest point and in the vastest expanse.
When we say "God is present everywhere," we mean all Three of the Hypostases of the Trinity. They cannot be separated One from Another. Where the Father is, the Son also is, and the Holy Spirit also is. So, Christ is everywhere, always.
Yet, to be "present" may mean two different things. God is everywhere, but when we say that Christ is "present" in the Church, or where "two or three are gathered in His name," etc., it means not just His existence, but His action, His "doings" in the Church, in our midst. Christ is present in His Church not exactly in the same sense as "Christ is present on a remote un-inhabited island in the middle of the ocean." Christ DOES something in our midst when we gather for the Divine Liturgy or when we are partaking in the Holy Mystery of Confession, etc.