Make sure you do not run them with the cover on or you could hurt something in the long run but you can cover them any other time you want to.
heat
i only use my stereo on sundays for 6 hours. i recently started to put paper towels above the air vents on my pre amp tuner and power amp to keep the dust out. i have a mcintosh mx132 and mc602. is this a bad idea? i know heat is the worst enemy for electronics but i don't play it loud anyway!