Nice bike. Which color scheme do you have?
Those left and right-side engine air scoops direct air towards the rear cylinder head for cooling. Even the small one on the right is functional.
As for the air intake, directly in the front of the plastic airbox cover is a screened area that serves as your fresh air intake (yes, by the fuel cap). The black airbox underneath has several cutout regions. Unless your going for maximum power at full throttle, just switching to a K&N filter is plenty to improve airflow. Depends on your goal I guess. Unless your street racing or going to the track or strip frequently, the stock airbox configuration is fine.