Mike, a couple of things I've learned about dust extraction: If using a low velocity, high volume device (typical 4" dust extraction), allow for plenty of airflow. Dust and wood shavings are dumb and bashful, they like to hide in the corners and stay there. Hard, non-porous surfaces allow wood byproducts to flow more freely into the dust containment system (think metal or hard plastic).
If you wish to mount the dust extraction opening on the small end of the box-fence, allow for some type of air flow opening on the opposing end. When the bashful pieces are hiding, you can always prod them along with a burst of compressed air towards their happy home.
Sawdust is not dirt