There is no contradiction between the passages that speak of Allah’s being “with” His creation and those that speak of His exaltedness above the Throne.
Let no one imagine that these texts ever conflict with one another. Someone might claim, for example, that the Qur’an and Sunnah affirm Allah’s being above the Throne, yet this seems outwardly opposed to His statement, “And He is with you wherever you are” (al-Hadid 4), or to the Prophet’s words, peace and blessings be upon him, “When any of you stands to pray, Allah is in front of him,” and the like. Such a conclusion is mistaken.
The truth is that Allah is genuinely with us, and He is genuinely above the Throne, exactly as He Himself has joined the two descriptions in His words:
“He is the One who created the heavens and the earth in six days, then rose over the Throne. He knows what enters the earth and what comes forth from it, what descends from heaven and what ascends therein. And He is with you wherever you are, and Allah sees whatever you do.” (al-Hadid 4)
Thus, He informs us that He is above the Throne, knowing everything, while being with us wherever we may be—just as the Prophet, peace and blessings be upon him, said in the hadith of the mountain goats: “By Allah, He is above the Throne, and He knows whatever you are doing.”