Chapter 5 is about making the fuselage sides as outlined in orange in the picture below. There is more to it than that. In this chapter, you also install the longerons, upper longeron stiffeners, lower aft stiffeners, LWX and LWY pieces (they serve as the main landing gear attach points, rear seat support and center section spar attachment points).
The idea here is to make two fuselage panels (with the longerons installed). The cutouts that are shown here are not cut until proceeding chapters later on. Only the inside of the fuselage panels are glassed at this time. The outside is glassed after the fuselage has been assembled in Chapter 6.
The inside of the panels are glassed flat. After they are built, they are force bent (in Chapter 6) around the bulkheads as shown in the picture below. This gives the Long-EZ its rounded body, rather than ending up like a square shoe box.