Silmarillion - Ainulindale

[Raynor]

We are told that the Children – Men and Elves – entered only in the third theme; what then is the significance of the Second?

In the Ainulindale it is stated that:

But Manwe was the brother of Melkor in the mind of Iluvatar, and he was the chief instrument of the second theme that Iluvatar had raised up against the discord of Melkor; and he called unto himself many spirits both greater and less, and they came down into the fields of Arda and aided Manwe, lest Melkor should hinder the fulfilment of their labour for ever, and Earth should wither ere it flowered.

I believe that the second theme reffers to the period starting from the actual begining of Ea up to the coming of the elves (~1050 valarian year) [or, maybe, up to the chaining of Melkor (1090 VY)]. During these period there occured the wars between the valar and Melkor, in which Manwe was, of course, the chief good guy.