What works on a server
Pocketpair's current server documentation says server-side mods work only on the Windows dedicated server. A mod must explicitly support server installation; check that its Info.json installation rules include server support before enabling it.
Place the Workshop files
The default server path is Mods\Workshop\[folder]\Info.json next to PalServer.exe. You can instead set WorkshopRootDir to an absolute path in Mods\PalModSettings.ini or pass the -workshopdir launch option.
Enable package names, then restart
Set bGlobalEnableMod=true and add one ActiveModList line per PackageName in PalModSettings.ini. PackageName comes from Info.json and may differ from the folder name. Restart the server to deploy the enabled packages and create their install manifests.
Update and troubleshoot safely
Restart after a package version changes so the server can replace the previous deployment. If a mod does not load, verify server support, dependencies, PackageName and the generated InstallManifest.json before changing anything else. The -NoMods launch argument is the clean isolation test.