Personally, I went the opposite way and removed the little black plastic pieces under the seat. My thinking is...more airflow under the seat will keep it cooler. By adding those side panels, when stopped on the bike there will be no airflow around the rear header and therefore all the retained heat will travel up under your seat and get trapped (around your wiring and battery and your butt).
I do wear adventure pants most of the time, with good leather on the inside of the legs, they deflect the heat really well.
1090R - Wingsexhuast