Hello SeonaidMack,
getting on the ferries from the water taxis is really easy, you do not need to worry. The ferries (and daytour boats, which is pretty much the same way of accessing them) have kind of a low step at their back, and the water taxi or zodiac has one, too - and when it approaches the bigger boat, it will be these two steps close to each other. You will always have one helping hand on the water taxi and one on the ferry/boat. It is pretty much impossible to fall into the water this way. (But you should wear comfortable shoes, no high heels, no flip flop sandals and so on.)
When I went with the Gaviota, which was a great ride, the captain did not start before everyone had put their life jacket on, these were provided by the ferry.
You can indeed fly to Santa Cruz from San Cristobal with Emetebe, but this will be with a stop on Isabela.
Hope this helps, happy travels!