You should just be able to run each instance using a separate home
folder, e.g.
syncthing --home=<full-path-to-a-folder>
and then change the ports under a few other settings (e.g. see https://forum.syncthing.net/t/best-fodlertype-settings-master-slaves-clients/19517/6).
Personally, I’d try run all that under the same account and avoid completely separate installations if possible, especially if the OS is responsible for the updates anyway. Not an expert here, but this would probably correspond to “creating separate systemd service files” if that’s how you start Syncthing right now.