Ecuador uses the U.S. Dollar. Bring bills in smaller denominations. $100 bills are not accepted in the Galapagos or Ecuador.
The Banco de Pacifico is on the road towards the Darwin Station. It gives cash advances, changes cash or cashes in travellers' cheques. It will not always work, so bring at least enough money to survive the first few days.
Banco Pichincha has recently opened a branch on the road heading towards Baltra. The lines are normally much shorter than at Banco de Pacifico making it easier to get cash advances or other transactions.
There is a Banco Bolivano ATM machine located in front of the main dock. As with some ATM's in Ecuador you are limited to a $300 per transaction limit and you may need to do several transactions in order to get the amount of money you desire.