i use gore oxygen covers. they zip up the back and cover all but the very bottom of the boot leaving the cleat and heel exposed. a massive improvement over my LG winter boots that just aren't as insulated as the softshell covers.

i use a bit of electrical tape inside the boot to cover any toe vents left exposed underneath, also. for extreme cold, 26 or below, i'll throw in a set of toe warmers since my commute is about 13 miles. during the warmer months it's not a big deal, but keeping your foot a bit active in the boot(wiggling your toes, finding different pedaling positions) will increase blood flow and keep your toes warm, too. seriously cold toes and feet can ruin any ride.