You should use only web.config if you need to change services after compilation . This should not be considered a default scenario.
This means that in most cases it would be better to resort to Code as Configuration , for example:
container.RegisterType<Service>();
container.RegisterType<IUnitOfWork, MyUnitOfWork>();
container.RegisterType<IMyRepository, MyRepository>();
XML, - . Unity .
, :
<container>
<register type="Service" />
<register type="IUnitOfWork" mapTo="MyUnitOfWork" />
<register type="IMyRepository" mapTo="MyRepository" />
</container>