I can only describe how it works in our company. Normally seat allocation is left totally up to the check-in agent. They are asked to periodically check the bay split to ensure an even(ish) spread. If the booked load for a flight is low, then the loadcontroller or dispatcher will weight restrict the bays. This means that only so many seats can be used in each bay which will influence the seating distribution. Our Departure Control System is capable of automatically allocating seats(although we never use it), all that needs to be specified is window or aisle.