Sebastian,
As far as I can tell, the general idea is to handle specs, TCKs, and implementations, each on their own.
No process has been yet determined for any of them, though.
We're currently trying to decide a brand for one of the components (the umbrella spec that will contain all the other specs), and these are pretty much the first (less than a) dozen projects that have been entered to EE4J, in order to do whatever we need to migrate them. This will, probably, involve a lot of code refactoring, and documentation being written or shuffled, as we try to move these projects into the new structure.
On the "Eclipse" naming issue, my understanding of the foundation's project naming conventions is that you are not under any obligation of adding the "Eclipse" brand to the project name. When referencing the project, however, it's strongly suggested it be done with the brand as the first word.
"Project Name", Eclipse "Project Name", "Project Name" Project, and Eclipse "Project Name" Project are stated to be interchangeable at will (at least for most situations).