This is NOT an answer! Sorry! But I have the same goal and was wondering if you had figured this out.
To reiterate: The goal is to "Get Books" through Dropbox and have them auto-sort into Marvin custom collections based on custom column metadata created in calibre.
A little more information on the situation: In Calibre, I have books sorted by a custom column "Fandom". I use the "Series" for traditional Series (Song of Ice and Fire) so I don't want to move this information even though that means I can use the pre-existing Smart Collection "Series".
When I first uploaded to Marvin through the Calibre connection in "Get Books", it very intelligently created Custom Collections based on the Fandom and auto-sorted all the books. It was awesome. Again, this is when I was corded to my pc and manually connected through the Marvin app.
However, I mostly use Dropbox to upload these days and this extra metadata (as well also word counts) does not seem to move along with it. I feel like it the answer is there because, when connected through Calibre, it did it without even being guided by already-made Custom Collections - it just did it and it was, repeat, AWESOME.
So, yes, that's what I've been fiddling with. If you (or anyone else!) has figured this out, please share. Marvin is the absolute best hands-down ereader and if I could do this, then truly all my dreams will have come true.