Depends on port.   most we have used you just bypass the check in desk bit the rest of the boarding path is the same Security etc.   Sometimes they have multiple boarding gangways but often just one and those getting off squeeze past the ones getting on.   Lisbon main terminal once upto the boarding level there is security then a duty free then you walk to the ship. Can't remember where the check-in would be as it has always been a port visit not embark.