Content/Libraries is not a standard directory within an app bundle; use Contents/Frameworks instead (.dylibs are allowed in that directory just the same as .frameworks).
Set the Install Name of each library to @rpath/libWhatever.dylib and set the Runpath Search Path of the executable (in Contents/MacOS) to @loader_path/../Frameworks.
For library interdependencies then Runpath Search Path will need to be simply @loader_path so dependent libraries can be loaded from the same directory.
EDIT: People might find the copy_dylibs.py script in this repo useful for copying third-party .dylibs into the App Bundle. It recursively hunts for libraries that need copying and corrects the Install Name of the libraries as well as code-signing them.