You need to clarify some things. Did your bike come with the cover? If not, the infill panel is available from aftermarket sources for the non ES bikes. The Yamaha factory part, (Cover, Side 2, 2KB-21721-00-P0), probably won't fit correctly unless you have an ES bike and it's just missing.
On the factory part there are two plastic rivits on the bottom edge. This type of fastener is used all over the bike. To release, you press the center in with a pointed tool like a phillips or JIS screwdriver, then you can lift the edges and pull the loose fastener out. To install it, you press the center pin back out so the center head is raised. (it has notches that you'll feel when you move it), then install the fastener in the panel and hole beneath it, press the center pin flush to lock in place.
There is also a plastic pin on the top inside edge of the panel to the rear that fits into a hole and a flange bolt on the bike frame to the front that the panel slips down onto before you press the lower side of the panel in and secure it with the plastic rivits.
edit - if you bought an aftermarket cover, it's usually just held in place with the two bolts on the rear foot peg bracket and maybe a zip tie or two at the top around the subframe.