That is a great question. If you look at the example for Hal you will see that the rels are defined within the context of the sub-resource.
I do not know of any definitive guide on when the rel is related to the resource as a whole or a contained sub resource.
The only extra piece of information I can point you to is the anchor parameter in RFC5988 which allows you to redefine the context IRI using either a fragment or a completely new URI.
Ideally, your mediatype should state whether the context IRI is different for nested resources, or whether the context IRI needs to be explicitly changed. That would be another advantage of using a media type like application/vnd.hal+json instead of plain old application/json as the Hal spec states:
@rel – For identifying how the target URI relates to the ‘Subject
Resource’. The Subject Resource is the closest parent Resource
element.