After the layout sat on my desk for a couple of days, I went back in and tightened up areas that didn't look right (it's good to have some time to gain perspective) and then I take a lead stick holder and use the side of it to lay down my black areas. To add form, shadow, indicate texture but most importantly, to create depth and a feeling of light and 3-dimensionality. I squint a lot during this process to make sure the black areas are forming the basic shapes I want to create.
After I chunk in the blacks and squint to make sure the shapes actually form different planes and essentially look well balanced and composed aesthetically, I go in with a .5mm mechanical pencil, HB lead, and start capturing and better defining shadows and add detail and rendering. I work left to right sometimes so that I don't smudge any of the final pencils.