I've been reading that thread, but not having a Kindle, it's hard to even discern what difficulty you are having. Are you saying you directly access Calibre's Library folders, or just that you prefer Saving to Disk first, then drag/drop?
He created 15 folders on the Kindle that he's using like 'Collections'. He manually moved his 300+ books into those 15 folders. So I think his issue is that his book list in Calibre doesn't have the tags to correspond to those folders (instead he has the plethora of junk 'download metadata' tags). So once the K2 driver can handle collections, he's afraid when he syncs, it will reorganize his nice 15-folder library into the junk tags that were downloaded with the rest of the metadata.
@Bluesman: The ideal solution to your problem would be to wipe all the tags from your Calibre library, and then add tags that correspond to the folders you created. Obviously this is in essence re-doing the work you already did, but it might be inevitable.