Say we have an application which consists of one executable and 5 libraries. Regularly all of these will be contained in one directory and the libraries will be loaded from
To make automatically copy the assemblies to the folder you want them to be in, you could set Copy Local to true for all of the references, and make a post-build step to move them into subdirectories.
Alternatively, you could set Copy Local to false, and add the referenced DLL files as files in the project in the appropriate subdirectories, and set Build Action to Copy to output directory (This will preserve subdirectories)
The most flexible way to make the runtime find them is to handle the AppDomain.AssemblyResolve event and manually load the assembly using Assembly.LoadFile. You would need some way for your code to know which assemblies are in which directories.