In a Multi-AZ setup, any change you make to the instance will first be done on the standby instance. Then, failover will occur (during this phase your application won't be able to connect to the database) and the change will be applied to the primary instance. The failover is the only downtime.
More information: http://docs.aws.amazon.com/AmazonRDS/latest/UserGuide/Concepts.MultiAZ.html