So I played a bit. And here's how you can use both Calibre or Kranf.
Kranf uses the folders under \documents on your Kindle to decide where a book should be in Collections.
So, here's how I made Calibre respect that folder structure. My custom column is "kindlecollection"
after rearranging and updating collections using Kranf (so all my books are in subfolders), I re-imported collections into Calibre. In Calibre, under Preferences, "Sending books to Device", this is my template:
{#kindlecollection}/{title} - {authors}
since my user/custom column is kindlecollection, all I have to do is populate the user column 'kindlecollection' in Calibre; then when I send it to device from Calibre, whether I end up using Calibre to update, or Kranf, either way the collection is honored.
One irritating thing about Kranf, I do have a couple of ActiveContent things. Kranf just puts those back in the root (not in a collection). So for that reason alone I may use Calibre more often for Collection updates. Obviously this is still early in my testing of what I prefer; I may change my mind in 10 minutes.
