Okay, i got it working.. I guess since space engineers is crap, i have to use SESE to allow autostart of the instance.
Using the Space engineers server extender exe as executable.
I am using the UGCC Local Broker, it does not work without this. And all i have for command line arguments are autostart instance="server"
I will just have to add the ugcc to the service list so it starts up with windows. Can now start/stop server from panel.