JRiver uses the word "Library" to mean "Database" mostly. But they also mean "the music folders and files".
The database files should always be in their own folder, all by themselves. Music (or other media) should be in a separate folder, or folders. You can control what is auto imported by setting up one or more folders in the auto import area:
Tools > Options > Library & Folders > configure auto import
I'm not sure what your "sweeping" process is, but I suspect this is part of the issue. If you let MC import files from a particular folder (new music) and then manually move them (with an external program or process), MC will lose track of them. You can kinda fix that with the "fix broken links" option. But what you really want to do is to have MC move the files and folders for you. The Rename, Move, and Copy Files tool can make this very easy.
But I suspect that I'm probably asking you to change too many things about your process, all at once. If you are interested, I can try to help some. If not, I will just wish you good luck with your old process.
Take care,
Brian.