Rob, some things to consider,
1. Over processing - it's one of the 7 wastes of manufacturing. The box for the drawer is not needed. All you need is drawer sides aligned to the drawer opening. They would add enough strength to the case. You can add the runner after the fact. Then just route a groove in the side of the drawer to run on the runner.
2. How are you going to attach the box to the front and back of the case? Hang it from the top? The top will move and it won't align with the drawer opening. You can't just glue it in place. If you use dowels or tenons (even loose ones) you have to do that at the same time you are putting the entire case together.
3. If you make these boxes, then you will have to notch them out at the top to allow room for the pencil drawer from the side. I'm assuming the depth of the pencil box will be such that it would run into the side of the box or even a drawer runner as I suggest
Shaun