Sorry but I can't be of much help. I've not taken Megabus myself but my dd used to ride it regularly. She, however, was riding alone so we never worried about the seating.
Depending upon the day, time and route the bus ranged from nearly full to nearly empty.
In our city people were just all sitting and standing around the area of the bus stop until the bus actually arrived and then they formed a very free-form line. It was not structured at all. If the bus was early almost no one got in line, if it was late everyone rushed to get in line.
Megabus always worked great for my dd - hope it does for you as well.