Upload from the game
Server Manager → your server → Manage Saves → Upload Save → pick a save from your PC. Then Load it. This is the normal way and works for single-player and co-op saves alike (co-op saves keep everyone's progress; players get their character back on join if they used the same account).
Where saves live on the server
.config/Epic/FactoryGame/Saved/SaveGames/server/ holds <SessionName>_autosave_1.sav and your named saves. You can also drop .sav files there with the Files tab (server stopped), then load them from the Server Manager.
Save name and session
A session groups saves; the auto-load session in Server Settings decides what the server loads on start. After uploading a save from a different session name, set auto-load to that session or the server starts empty.
Download
Server Manager → Manage Saves → Download, or grab the .sav from the folder via the Files tab / SFTP. Keep one on your PC now and then.