As I've recently been reading about the nature of time and the nature of the Trinity, I have found Paul Helm's work to be good reading. For instance, he notes in God and Time: Four Views (pg. 33):
...the affirmation of God's timeless eternity appears to be necessary in order to avoid difficulties in affirming the eternal begetting of the Son by the Father; for if God is in time then the begetting of the Son looks like an event in time.
If the begetting of the Son is not an event in time, it is atemporal or timeless. But if the begetting of the Son is an event in time, then it seems that there was some time prior to the generation of the Son in which he was not generated. More precisely, the Son is not necessarily pre-existent. This leads to some bizarre conclusions: for example, "fatherhood" would be an accidental and acquired rather than an essential property of the first person of the Trinity. In fact, it would seem that pre-existence would be a and the only property that would be essential to the first person of the Trinity on this view. This would amount to a sort of reverse Arianism. It at least underscores the problems of a notion of time which infinitely extends into the "past."
I say all this to note that if one accepts eternal generation (and even if he does not), he must either accept divine timelessness or reject a host of classical Christian doctrines like divine immutability, the pre-existence of the Son (seemingly), and especially eternal or intuitive omniscience.
Helm provides a positive formulation for understanding eternal generation in the context of divine timelessness at the end of Eternal God (pgs. 284-286):
...while it may be granted that ‘begotten’ has a meaning distinct from ‘created’, that meaning is not wholly distinct, in that both ‘create’ and ‘beget’ are causal notions. How can the Father beget the Son without adversely affecting the equal divinity of each and the divine unity of the pair? It would seem to follow from being begotten (however this is understood) that the Son cannot be equally divine with the Father, in that he cannot be autotheos.
Perhaps it is possible to address these questions in the following way. For an atemporalist the eternal begetting of the Son by the Father cannot express a temporal relation of any kind. The Son cannot come into being at some time after the Father, nor (of course) can he come into being at the same time as the Father...
The nature of the begetting must be something like the following, then: there is no state of the Father that is not a begetting of the Son, and no state of the Son which is not a being begotten by the Father and necessarily there is no time when the Father had not begotten the Son, and no time when the Son had not been begotten by the Father...
The residual problem is not, how can the Son be co-divine when there was a time when the Father was and the Son was not, but, how could the Son have a timeless relation of begottenness while being equally divine with the Father? Perhaps a solution to this may be found in expunging the language of subordination entirely from the account of the Trinity, in asserting the co-equality of the Father and the Son, not their equality in every respect, but their equality in respect of divinity. The puzzle (to me at least) is why a satisfactory Trinitarian doctrine may not rest with saying that God exists in three co-eternal and equally divine persons. Is the language of begottenness and procession not a reading back into the doctrine of the Trinity those roles which according to the New Testament each person of the Trinity adopts in order to ensure human salvation?
I am not quite sure what Helm means by "equally divine" or "equality in respect of divinity" in the last paragraph. I find it hard to believe the "solution" he means to offer is the rejection of the very doctrine of eternal generation which he defended throughout the chapter. So here's what I think he means:
In the first paragraph, he seems to think autotheosis is relevant to divine co-equality. He may be puzzled as to why eternal generation would preclude the idea that the Son can be autotheos, for which reason he suggests "expunging the language of subordination entirely from the account of the Trinity." His final question seems to imply that the Scriptural evidence for the eternal generation of the Son relies on analogy: we see the economic activity of the Trinity and use that as a lens for understanding the ontological Trinity. My best guess, then, would be that Helm is suggesting that this lens should not be used to read the language of subordination which may be found in the economic activity of the Trinity back into the relations between the persons of the ontological Trinity. Thus, the Son may be autotheos yet eternally begotten.
If this is an accurate rephrasing - and if it's not, the apparent alternatives puzzle me! - it doesn't strike me as satisfying Helm's own earlier question: how can the Son be autotheos if he has been "caused" by the Father?
Regardless, I think Helm does a good job of explaining how eternal generation can be consistent with a theological system which holds to divine timelessness.