I agree, limit his roaming space at night. What time do you wake up to take him out for his first potty break? My younger boy has a fast system and he often poops before bedtime, about 11 pm, and then again first thing in the morning, 6 - 7 am. Sometimes it is as early as 5 am, grrrr.
We use pads, but he wakes me up first so that I can take care of it right away.