Folders in the Library are there only for storage. All of your projects should be in the Collections panel if you imported correctly using the Plugin.So you could ignore/Hide the Folder's Panel and work with Collections(same as Aperture)
Please refer these Articles for more information
Thanks! I would however prefer to have my folders arranged in a similar manner so that I'll be able to sort out what's what in ten years or so. I am not entirely pleased with the date-based folder naming so if anyone knows of a way of sorting this out automatically I would be very thankful.
Perhaps the only way to go is by relocating originals in Aperture, switch to referenced and have Lightroom leaving the masters where they're at?