Shenzhen Shekou Port to Hong Kong International Airport

I am taking a Korean Air flight that departs Hong Kong airport at 12:45am on Sunday, September 15th. In order to make this flight, I would need to take the ferry on Saturday, September 14th from Shekou Port. Do you have to "check-in" for your flight at Shekou Port or can I just get on the ferry and then check in when I get to HK. Are there any restrictions on when I am allowed to arrive at the Hong Kong airport ferry terminal? In other words, can I get on a ferry in SZ and arrive Hong Kong airport as early as I'd like? Conversely, is it better to check in at the Shekou Port for my flight and how early should I arrive at Shekou Port in order to go through check-in in advance of the ferry ride?