pd2, as flightdeck we tell the cabin crew where to seat passengers in order place the aircraft cofg in the required position for take off. its important to have the actual cofg as close to the calculated one for take off for setting the stab trim for the rotation. once airborne you're free to move around the aircraft as we 'feel' trim changes and correct as required. our load sheets are designed in such a way that we split the cabin into sections or bays. of course the aircraft would fly if one or two passengers weren't in the required bay but its a legality issue. the loading of the aircraft MUST reflect the load sheet.
the check in staff often wont know if the aircraft is carrying cargo or the weight distribution in the holds (which often arrives at the aircraft first and therefore is loaded much earlier than the passengers). so will allocate seats in a standard fashion. once we're passed the passenger figures and complete the load sheet we may find that the passenger distribution is incompatible with the hold weight distribution. its much easier to ask a passenger to move than it is to move bags or cargo.