It's well worth paying a little extra and going for the business class option with Supercat, meaning your on the upper deck of the boat with more room and better quality seats. Business class also included a Coffee and small snack as part of the deal.
They ask that you get to the Supercat terminal around 45 minutes before the boat leaves, and the earlier you get there, the better chance you have of getting a good seat on the boat. When you go through the check-in and security area, you also get shown a seating plan of the Supercat ferry, so you can pick your desired seat. They then write the selected row and seat number on your ticket, and then it's just a matter of waiting to board. The terminal has plenty of seating, and normally a few TV's to help make the time pass a bit faster. You will also find a small kiosk or store selling food and drinks, and the Cebu terminal even has wifi available for a small fee.