In other words, Aquinas recognizes that there is a possibility that the cosmological argument could support two different interpretations: God could be understood as the initial cause of all events in the universe (horizontal account). The problem with this is that it does not guarantee that God still exists (he might have died long ago) or that God is intimately involved right now with the world (he might have created the world and then ignored it subsequently). There is also the possibility that the universe might have always existed (after all, if this can be said of God, why can't it be said of the universe too?)--in which case, the existence of the universe right now is explained by a sequence of caused events stretching back endlessly.
To handle these concerns, Aquinas proposes a more vertical account: rather than thinking of cause in terms of time, he proposes that we think of cause in terms of being or existence. For something that is only contingent (dependent) to exist right now, there must be something that exists right now to account for its existence. If that thing, in turn, is contingent, then something else must exist right now that accounts for its existence, which itself is accounted for by something else, and so on. But this vertical sequence (unlike the horizontal sequence) cannot go on endlessly because that would mean that ultimately nothing would account for why there is any particular thing right now (since the ultimate cause would itself never be identified as existing right now). That is why there must be a first (necessary) cause that exists right now that accounts for the existence of all contingent causes. [Ultimately, then, the cosmological argument seems to be based on the ontological argument.]