You need to cross the Itabaca Channel, from the airport, which is located at Baltra island, to Sta. Cruz island, then take a boat to come to Isabela island. (for more details visit our website)
You need to booking an early flight from Quito or Guayaquil since the boat that is coming to Isabela island from Sta. Cruz is at 2 pm. If you are thinking to get Chez Manany in the same day.
There are 2 boat schedules to get Isabela from Sta. Cruz, one is in the morning at 7 am and the second one is at 2 pm.
The time you need to get to Isabela island from Sta. Cruz is 2 hours to 2H30 minutes, depending of the weather.