So the jar was emptied, the pebbles, sand and gravel sorted into piles and they started again. This time, they started with the pebbles, then fed the gravel into the spaces around the pebbles, then finally the sand which duly trickled into the tiny spaces around the gravel. Everything fitted neatly into the jam jar.
It's a metaphor for editing. We need to sort out the big stuff - the plot holes, the pacing, the character arcs - before we can start worrying about the paragraphs and sentences, let alone the individual words.