It seems like you are asking for two things there so I’m not sure where the actual problem lies.
You can simply drag files to iCloud Drive which is in the Finder sidebar by default. If you frequently target a specific folder inside of iCloud Drive, you can add that the the sidebar as well, for convenience.
If you want stuff auto-filed, then one of the automation apps will work fine for monitoring or targeting iCloud Drive folders. I have Hazel and one of my rules finds image files and PDFs in my download folder that are over a certain age and moves them into my Pictures (shared) and Documents folders in iCloud.