Not sure if you meant Megabus is "relatively cheaper" than other bus lines, if so, that's often not true. Over at Busbud we do price research on buses, including Megabus. Bus companies are using ever-more high tech pricing systems that monitor demand and competitors' pricing.
I just did a quick search on Busbud for cheapest DC - NYC bus for Weds, Sept 6th: the cheapest result on Busbud was Ourbus for $12.25 after non-optional fees ($12+fees), beating out BoltBus, Greyhound, Washington Delux and GoBuses. On megabus.com the cheapest is $16.25 after non-optional fees ($13+fees). Just wanted to point out shopping around can be useful. Of course the varied quality of service, stops, and amenities might make something other than the cheapest most attractive.
From first hand experience, I can confirm Spehro Pefhany's answer that the rest of customers can claim seats on a first-come, first-served basis at departure. At bigger stations, passengers line up for boarding and get to claim seats as the board. Things can get awkward if you have a reserved seat but someone else decided to take it anyhow, Megabus drivers have a lot else to deal with, an especially high number of passengers to process and often are hard to get the attention of for helping to clear up the situation.