To get the assemblies in a sub-directory you can copy them there manually, use a pre- or post-build event or something completely different.
To load them, you can use the AppDomain.AssemblyResolve Event, or (as noted by TomTom) the Element. From MSDN:
The following example shows how to specify application base subdirectories the runtime should search for assemblies.
The GAC is of course another place to dump your assemblies, but that wouldn't really count as a sub-directory... unless you install your application somewhere it really shouldn't be installed :P
