At the time of writing, the JSONAPISerializer does not provide a way to save a model with its relationships. You can save the type and ID of a relationships by customizing the serializer with a attrs-property, but this will not include any data of the related model, e.g. properties like names, ip adresses etc.
This feature is necessary for extensions (updating models in the backend-extension) and probably for the core at some time. Unfortunately, it is not considered in version 1.0 of the JSONAPISpec, hence the missing the feature in the Ember serializer.
There is a discussion that notes this feature ("Determine critical features for 1.1."). Thus, the Ember Data team will probably implement it when JSONAPISpec 1.1 arrives.
As workaround we can use the Ember-Data-Save-Relationships-Addon. The JSONAPI-Converter of the backend correctly converts the embedded properties in related models.
When JSONAPISpec 1.1 arrives, we will need to remove possible uses of the workaround and use the native approach of the future serializer.