What version of LabVIEW are you using? If you are using 2009 or above, there is an option to use the 8.X format for the executable. It is one of the advanced options in the build specification. You do NOT want to do that. In the 8.X format, the VIs are saved in the executable as a flat directory. This means that any VI that was named the same, regardless of library association, would conflict. This would cause those libraries to be saved outside of the executable.
If you are using the newer format, the executable keeps a directory hierarchy, just like a zip file. So you won't have the name conflicts in that instance.