Although you can throw almost any junk into a Mac application bundle, much good will not come to you.
If I understand right, you have both a Mac Application (bundled normally) and a side-application you call the "Assistant" you want embedded in the same application bundle.
You also mention libraries (.dylib's I guess) that must reside in the same directory as the assistant.
Now - if these libraries are only used by the Assistant side-application, I would recommend that you bundle the assistant as a Code-bundle (Apple provides lots of information about these, and you have easy to use templates from Xcode). You can then use Xcode to copy it into the right place within the main application's bundle (I'd choose "Plugins") and use NSBundle APIs to launch it.
However, if those .dylibs are shared between the main app and the assistant - then I'd say go ahead, stick your assistant, .dylibs and main app's binary files in the same "MacOS-X" directory, and use posix APIs, or shell command to launch the assistant. Of course it will share (if possible) every resource of the main application, because they are located at the same place. However, the main app's bundle can only have ONE CFBundleExecutable entry, and that should point to your main application's binary.