We decided to book everything with Costa through our TA and through Costa website.
This was good and bad. Good because of the flight/transfers because this way we had nothing to worry and because we got a deal that offered us the X1 drinks package (excellent for those who don't drink alchool like us). Bad because due to the Bahrein cancelation due to the unrest overthere the tour package we had booked suffered so many changes that we ended at tour desk more times than intended when booking tours online.
Flights were with Lufthansa but because we had to go from Portugal to Dubai this was the schedule: 6AM OPO-FRA (2.5h) - 2PM FRA-DXB (5.5h). Getting to Dubai around 11.30PM we had another 60' to pass through passport control and then 45' of transfer (getting to bus and travel) to Port Rashid. With the checkin to Deliziosa going smoothly we ended up on cabin around 2AM but still waiting for our suitcases. Fortunately Costa had some snacks on the Cruise terminal while we were checking-in and the Pizza restaurant was open on-board. Got to a deserved bed rest around 4AM. After this we definitely deserved our vacations. The retirn flight was a little easier since DXB-FRA was around 2AM so we ended up sleep the entire return trip :).