The GEARBOX system is installed underneath the glass, most commonly installed when the surfboard is laminated. The process involves routing the holes for the boxes first, then, when it is time to laminate, the board resin is poured into the cavities, and the boxes are installed. Finally, the lamination begins immediately over the boxes. For more details on the installation process, visit this site's INSTALL GUIDE.
The boxes can be installed after the board has been laminated in certain circumstances, but they will still need to be capped with glass to complete the installation. This is most commonly done when a board is being retrofitted with GEARBOX or if a box is being replaced due to damage. However, this approach could also be utilized when the board is colored, and you do not want the color over the boxes.