Hi Scarlett,
Cloud Manager does not manage the provisioning of EBS volumes, so increasing storage is something you'd have to plan and administer yourself. With a replica set environment you can maintain availability by upgrading one secondary at at time until you eventually step down and upgrade the former primary.
If you are looking for a more fully managed solution, you may want to consider
MongoDB Atlas. MongoDB Atlas is a database-as-a-service that takes care of underlying provisioning and configuration management. With Atlas you can adjust storage capacity and other provisioning/deployment options through the management interface -- changes will be deployed automatically with minimal downtime.
Regards,
Stennie