On the server, type this into the console:
exec("Add-Ons/Server_MyAddon/server.cs");
If the add-on was installed after the server started,
discoverFile(%file = "Add-Ons/Server_MyAddon/server.cs"); exec(%file);
Note that any add-on the loads weapons, vehicles, ect. won't work, due to the fact that datablocks are no longer allowed to be created.