I use Velcro to attach the lids to the desks. Pencils are almost never on the floor in my classroom anymore. This is one of my most favorite features in my room. I save the lids and ask parents to save them. You need to use tall skinny ones like on Great Value laundry detergent. Then the pencils don't lean over to far and get snagged on every passing kid.
Next are my "pouches". I purchase work order pouches from the office supply store and Velcro them to the sides of the desk. Only unfinished work goes in these pouches. That way I can tell who has unfinished work and I can redirect them to complete their work before heading out to recess or moving on to a center. This has worked very well for me. No more lost papers in the depths of the desk.