In the main window you can edit and arrange the clips or song if you prefer.
In the “double-click window” you get to edit what’s inside each of those clips.
You can’t do audio or midi note editing from the main window, just crop, repositioning and basic levels.
Think of the clips as containers, the audio is inside. Cropping a clip doesn’t crop the audio inside, but the edits you do after double-clicking an audio clip will be applied to the audio file (and be permanent).
This is kind of a basic explanations, but you’ll probably get the point.