I checked the wt.sysadm.administrators property (was ok), so went ahead and tried the URL to stop and start. Stopping the method server didn't look like it did it, but stopping the Server Manager worked. And then I started it using the link as well. BUT after I the server manager and method servers get started, The System configurator goes to an error page. So does that mean I can stop and start only one time from the URL before it gets restarted on the server itself or there must be something wrong in some properties? (I have only tested this on the test system).
Are there any issues or concerns with starting them all (Apache, Tomcat and Method servers) as a Windows Service?
I would start them all as services. I think Windchill must be set up to run as a service if you want to use the System Configurator page to start it. Otherwise, it's trying to open a command prompt in which to run.
I like the System Configurator page for those circumstances when you can't get on the machine (directly or remotely). However, with VPNs and good remote access tools, that is becoming less of a need anyway.
One more note on the System Configurator page. You don't need to have the MethodServer running to access this page. Only Apache and Tomcat need to be running to serve the page.