Usually I create a registry class in my web project, where I link everything together with StructureMap. See this: http://structuremap.github.com/structuremap/RegistryDSL.htm
If you have projects in your solution that have a lot of their own configuration, then you might want to provide these projects with your own registry, but don't really register it before the start_ application in global.asax.
Part of the IoC is waiting to bind everything together until you need it. Thus, it is more customizable. Therefore, if you can keep your registry on your website, you will have maximum flexibility.
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