Last year Mac OS Mojave introduced Stacks and if you haven’t tried it yet you should. Stacks allows you to auto clean up your desktop and keep your files organized instantly (animated gif below).
Additionally all users can modify how you can organize and group your stacks with any of the following organizational styles. I recommend stacks by “Kind” as this will sort your pictures, pdfs, docs, etc for easy access and to eliminate the clutter on your desktop.
- Date Last Opened
- Date Added
- Date Modified
- Date Created
Randomly if you use stacks and do not see a file you have on your desktop, just turn stacks off and then back on. This should resolve missing any files that should be stacked.