These copies of Agkyra are preconfigured to work with your ~okeanos account.
When you first run Agkyra on a system, you will be asked for your ~okeanos credentials as well as the local directory to be synced. The rest of your essential settings (e.g., ~okeanos URL, SSL certificates) will be pre-set so that Agkyra can work seamlessly.
You are free to modify them, as long as you know what you are doing.
By default, Agkyra is set to use your "pithos" container (the default place to store your data on Pithos+). If you keep this setting, everything in your "pithos" container will be downloaded at your local directory. If you don't want this to happen, you have to type a new container name in the corresponding settings field and Agkyra will automatically create it for you and use it for syncing. After that, you won't have to worry about storage containers.