Supplies inside a desk is like planets being sucked into a black hole! My students keep their supplies in the corner of their desk in a cup. They no longer have to search under books and inside of folders for a lost pencil. I put Velcro on the bottom of each cup and a strip of Velcro on the corner of their desk. These are the same cups and Velcro I have use for two full years now and I haven't had to replace any yet! I bought adhesive backed Velcro and cups from Dollar Tree (4 cups for $1).
I have my students add about 3 pencils, an eraser, a glue stick, scissors, a pen, and a dry erase marker to their cup. These are supplies they use almost daily and they are on hand quickly. At certain points through the school year, we add (or take away) certain supplies. For example, when we are working on fractions, I have the students keep fraction strips in their cup. Keep the supplies to a minimum, but add the items that they need often. Other supplies that you might add would be highlighters or a few main crayon colors.
Now, what do we do with the rest of our supplies? I have my students keep them in a large bag inside a drawer that the kids have access to. I give each of the students a gallon size baggie with their name on it. We bag up all those extra pencils, glue sticks, markers, and erasers, zip it closed and put them in a drawer. My students know where their extra supplies are and are allowed to go get them when needed. This keeps the mess out of their desk and helps them stay organized throughout the year.
I hope you are able to use this idea and make it work in your classroom. It has truly saved me time and helped me keep my sanity because my students always (okay 99% of the time) know where their supplies are!