We did and end of season cruise last year which sailed back to Southampton so I can only comment on the going out bit. At Crete airport, which is quite small and cramped, you go through passport control, collect your cases then head for the exit where you are directed to coaches. Your cases are taken from you and you next see them in your cabin some hours later. The ship is only about a 20 minute drive from the airport.
At the cruise terminal you will have to queue (initially in the sun if it's busy so have a hat and sunscreen handy) to have your tickets and passports checked and also your credit card swiped for your on board account. You are then given your cruise cards which you all have to sign in front of them (so have a pen handy). Then you go through a security scanner and finally, after the obligatory photograph, you can get on the ship.
If you are there fairly early then it's worth walking into Heraklion and having a look around the harbour and the castle. It's about a 30 minute stroll and there are a few bars and cafe's on the way. Have a nice cruise.