for the best airflow across the motor, shut the vent doors. if you'd like to get the best airflow for your comfort, take the doors off. I do this every year during the hot part of the year (in la, that's like mar to oct

).
to do it, first remove the top cap, 2 x 7/16 nuts on the inside. if you have a liner, you'll have to pull them out. with the top cap off, there are 3 torx screws (t20) attaching the glove box to the lower. take those off, and the glove box and vent door will come off as one unit. take the nut off at the pivot, and remove the door. then reinstall the glove box, and top cap and you're done.
I do this with the lowers on the bike, you just have to tilt them back a little so that you can reach the torx screws.
also, you'll notice that there is a 'guide pin' on the glove box that fits into a slot on the vent door. my vent door had worn a groove into the guide pin so I used a little jb weld to fill that in while I had them off.