I don't think there would be any substantial deviations from how a diurnal species would manage it.
Standard farming activities (building, plowing, watering, planting, harvesting) can be performed at night as well as during the day. We do it during the day because we're diurnal, not because it's a requirement.
Diurnal pests aren't substantially more common or problematic than nocturnal ones (as anyone who has woken to a ravaged garden can attest), so again, you'd deal in pretty much he same way - fences, scare crows and other deterents, and if needed forcing some poor schmuck to stand guard all day.
As far as domesticated animals go, I suspect they would favor nocturnal animals for basic ease of handling (it's a lot easier to take an animal out to pasture or milk it when it is awake).