We flew Avianca from LHR to Bogota and then on to Quito. Another 3-4 hours on the ground and on to Baltra airport in the Galapagos.
The Beagle sails 2 different routes. We chose this north west because we wanted to go to Fernandina and Isabela. The south east route goes to Espanola where the main attraction is the waved albatross but many of the other destinations were within day trip distance of Santa Cruz. The more remote route was more tempting.
From the Galapagos we flew to the coastal city of Guayaquil. It was a 4 hour bus trip over the Andes to Cuenca. A flight to Quito and local taxis and buses to Otavalo and the Intag Valley.