This bird is so powerful that its voice takes over the two places that really matter in this poem: the earth and the air.
Except, that's impossible, right? No bird is that loud. So maybe it's that the speaker is so absorbed, so captivated by this bird's song that it seems to fill up the whole world.
This poem is about nature, in a way, but it's also about how our minds twist and turn as the world flows in through our senses.
As, when night is bare, From one lonely cloud
Okay, so Shelley has gone totally simile crazy here. If he was writing today we'd probably need to have an intervention. ("Percy, we're all here because we love you. We just want you to lay off the analogies!")
In this case, he's comparing the skylark's loud voice to a single cloud in the night sky. By now, you've probably figured out that most of these images have to do with the sky in some way.
The moon rains out her beams, and Heaven is overflow'd.
Apparently the moon is behind this cloud, and filling the sky with light. In yet another striking, sky-related image, there's so much light that finally "Heaven" overflows with it.