Hades supports configuration at a project level. This is not something that Strange Eons supports natively, instead Hades creates a hades-project.json file in the root directory of the project.
Project configuration is to allow settings and configuration that more naturally belongs with a single Strange Eons projects instead of the current options of ‘global’ and ‘per card’.
To open the Project configuration do r-click Hades -> Project configuration
Encounter sets in Hades are always configured per-project. Encounter sets are created in project configuration, assigned a name, tag and icon.
Individual cards simply select an encounter set from a drop-down.
Collections work in an identical fashion to encounter sets, they are just a separate list.