I don't think it really matters if you keep the cover on or off, some people have said they keep it on to provide more even heat, but I don't know if that's true.

Those heating pads get pretty hot, it will probably be fine on low. In fact, mine is too hot on low, so I have it hooked up to a thermostat. A lot of people use dimmer switches to keep the temp from getting too high. Just make sure you test it out before putting the snake in the enclosure.