Agadeem's Awakening allows you to return one creature per mana cost from 0 up to X from your graveyard to the battlefield, not as many as you want. One per mana value. If there isn't a creature card with an appropriate cost for a mana value, you cannot chose one for that value. So for example, with X=3, you can return a creature card with mana value 0, a creature card with mana value 1, a creature card with mana value 2, AND a creature card with mana value 3. All the targets must have different mana values from each other.

Of course God Eternal Rhonas goes to the graveyard or exile first. How else do you expect the trigger to work otherwise? This is literally the trigger condition. When that trigger resolves you can choose to put it into the library. You are not dealing with a replacement effect ala Progenitus here. Which also means, the card can be intercted with while it is in the graveyard or exile until the trigger moves it to the library. And of course, the trigger only works when Rhonas goes to exile or graveyard from the battlefield. Mill it, and it stays in the yard.