End panels are installed after cabinets are joined and fixed to the wall.
The end panel should sit flush with the front of the doors, and are installed the same way for both base and upper cabinets.
Double check before you install that you have selected 28mm screws. With the overall width of your end panel and your cabinet, a 28mm screw will ensure that the exterior surface is not broken. A larger screw will pierce the visible side of the panel.