So you have never looked at the examples for Windows Phone... There are some pretty helpful insights how the Bootstrapper is put together.
There is a Configure method that is overridden to get the phoneservices registered, which is part of the Phone container that CM has in it.
public class Bootstrapper : PhoneBootstrapper
protected override void Configure()
container = new PhoneContainer(RootFrame);
with this you also have access to the Deactiveated, Launch, etc events but you don't have to really do anything in those events unless you really need to. The container is the IoC container built into the Phone assemblys of CM.