Allah is not the universe but its creator, and he is omnipresent but not in its physical sense.
Let me bring you an example. Imagine an infinitely large clean white paper, with only one single black dot on it, is place in your front close to your eyes. You don't see the borders of the paper, it is just too large, thus, if someone asks you what do you see You'll answer only a simple black dot! You will not report back a black impact on a white paper as you just cannot recognize the white paper from void when you are not able to see its boundaries (the paper's texture is assumed as invisible to your eyes). If someone paints the paper and then ask you what do you see you will describe the shapes drawn in colors but will never answer back a paper with some colors on it as you see the colors on the paper not the paper under color (again the paper's texture is ignored), again the paper would be understood not any more than void in the absence of intuition. This is a mere example to say if I am asked about what I see from when I get up in my bed in the morning to when I go to my bed in the night I can describe quite many things that I have seen that day but I just cannot describe the reality that nothing exists but Allah, we are all only some impacts owing our existence (not only first becoming to existence but also remaining existed) to His creation.
This was one example, now let me bring another example which describes the creativity of Allah better (although still in a translative manner). Suppose you stand in front of a mirror, do you agree that what you see in mirror does not exist at all? Of course there is no "you" behind the mirror, that's only "the imaginary you, mirrored". But of course you can describe what you see, the color of skin, the form of nose, the kind of clothing, the height, the fatness, the shape of face and style of hairs and etc. . Hey, you are just describing what doesn't exist in real! Similarly some Muslims believe that nothing exist but Allah. He is the only existence whose existence owe to nothing else (He is the true Needless). But then he will to create something, the creation for God is roughly like imagination for us, God creates just as He will as we can produce a whole imaginary world just as we will. All of us whose existence owes to the existence and continuous creation of Allah exist only to the extent that Allah will give us existence, to one in the form of a stone, to one in the form of a cat, and to another in the form of a human, angel or elf and etc. . He has created us but before that He has created time and space, material and energy and the rest of what we do need to exist upon, in any stage of our existence.
Anything that we see in universe is a sign (Ayeh) of Allah as it would have never existed if Allah was not existed and creating it instant by instant. Those who we call "Aaref-bel-lah" (knowing Allah better than others) are those who see Allah everywhere when looking around (Imam Ali AS has stated that I see no one unless I see Allah before him, with him and after him), not me and you and mountain and river. Allah is omnipresent but not in the sense that he has filled somewhere or not, neither he sits on a place called throne, nor he fits in any volume of his created universe, he is just beyond any of these concepts and the words used in Quran for him are most of the times TRANSLATIVE! Note this:
وَكَأَيِّن مِّنْ آيَةٍ فِي السَّمَاوَاتِ وَالْأَرْضِ يَمُرُّونَ
عَلَيْهَا وَهُمْ عَنْهَا مُعْرِضُونَ
And how many Signs in the heavens and the earth do they pass by, yet they turn (their faces) away from them! (Yusof:105)
Which states the signs of Allah and not his parts or body limbs as He has none.
He has no mass as He has created masses and materials, and spaces that masses fill, or time through which masses evolve, or energy and light which can be emitted or translated from a place to another place, and He is just beyond any of His own creations. His creations in his scale of existence never exist at all, they exist only in our scale of existence and by this scale I do not mean a scale for size but a scale for the reality of existence. When we say "الله اکبر" (Allah is greater) it means He is greater than to be described in words not bigger than everything in size, as he has no size and He is just not measurable with the measure of a non-existent universe.
Also note that Allah Himself is even beyond His names, as His Hosna names are attributes that work in relation with His created universes (our universe being one among many universes that He has created), be it Ar-Rahman (the most Gracious), Ar-Rahim (the most Merciful), Al-Ghahhar (the Irresistible), Al-Montaghem (the revenger), Ash-Shakoor (the grateful), and etc., he is just beyond all these notions and He is beyond the infinite limit of these notions as well (all these names would coincide in the infinite limit, even the Al-montaghem and Al-Ghaffar would be the same for Allah as Allah is one unique existence without aspects, He is not like a coin that may turn from one side to another side).
Next note that when a concept is beyond our imagination we can never coin a description to Him by ourselves, Only Allah himself can describe Himself, anything that we say about Him would be like Allah has stated:
No knowledge have they of such a thing, nor had their fathers. It is a
grievous thing that issues from their mouths as a saying what they say
is nothing but falsehood! (Al-Kahf:5)
Or something like this:
But they have no knowledge therein. They follow nothing but
conjecture; and conjecture avails nothing against Truth. (An-Najm:28)
That is, before He send a prophet we would never know if we are allowed to call Him Al-Montaghem or not, Al-Ghaffar or not, these are what we can say nothing about until Himself (who knows Himself and the only one who knows Him) let us know. Now we are introduced to His Hosna names so that we can call Him only through them, as He has ordered us in Quran as well. The only exceptions are those statements that instead of describing Him rather try to purify Him, like "Alleluia", "there is no god but Allah", "Allah is greater" and some few others …
People who don't know Allah well, but feel an attraction toward Allah, the Almighty, may ask Allah trough some names and attributes not actually allowed by Allah, but as long as they do not know the truth that will be ok, as they are not trying to lowering his grade from what He is to what He is not, they just don't know how they should call Him.
Anyway, Allah knows the best