Have you looked at the built-in Help and manual ?
Regarding sync, it’s covered in our documentation and there is a forum post on it: Sync Types Explained. This is a good place to start.
and then export it out to a clean version of iCloud or Drop Box
Why?
I was thinking about copping all the files that are in iCloud to A local drive and then cleaning them up/organizing them in finder as I would have access to Hazel, Houdaspot, keyboard maestro and Alfred.
Yes, cleaning up the data before import would be a good idea. However you do it, is your call.
Once I had the big database would it be possible to create the smaller databases directly without having to export/import.
Yes, you can create databases and move items between them.