I usually group my projects into working sets. When importing a Gradle project, it should be possible to assign a working set (i.e. an existing or a new one). This could be done from within the import dialog and pre-selected if you right click on an existing working set and choose “Import…” from the context menu.
Thank you for the suggestion we’ll definitely look into it. If you’d like to track the progress on this item we created a ticked for it: https://bugs.eclipse.org/bugs/show_bug.cgi?id=466855
The latest snapshot of Buildship offers a working set selection in the import wizard. You can install or update it from the http://download.eclipse.org/buildship/updates/snapshots/1.0 update site.
The working set feature is part of the released versions of Buildship.