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I wrote a blog post on how to do this using P/Invoke. Using the ServiceHelper class from my post you can do the following to change the Start Mode.
var svc = new ServiceController("ServiceNameGoesHere");
ServiceHelper.ChangeStartMode(svc, ServiceStartMode.Automatic);
You can use the OpenService() and ChangeServiceConfig() native Win32 APIs for that purpose. I believe that there is some information on pinvoke.net and of course on MSDN. You might want to check out the P/Invoke Interopt Assistant.