You'll run cooler with the lid open, but the keyboard leaves more air gap than if you were to place the bottom on a comforter. That really causes the case to lose thermal efficiency in radiating heat out.
There's several questions on this - look for temperature and closed clamshell mode
No - just that if they are needed, you want the air to not be constricted. You should be able to just use your eyes to see that the air gap isn't totally sealed.
i.e. don't place a paper folder on the top of the bottom case, etc...