Injecting AutoMapper profiles
What is the purpose of the IMapper interface and Mapper class?  It looks to me that they are just wrapping the IMappingEngine interface and MappingEngine class.  While this is a good method when you have a third party class that doesn't have an interface, I think it is overkill here.  Why don't you just use the IMappingEngine where you need that functionality?

If you are going to keep your Mapper class, I would rename it, having two Mapper classes is confusing.

As for where it is, I don't have a problem with doing it this way.  All the wire-up is done in one place, and its easy to find and add to as needed.