I believe Per Project is enabled by default and will apply to all new projects which are named straight away.
 
You will not have lost or orphaned your original recordings PROVIDED you open the cwp that DOES reference them and do a Save As immediately. In this case, you MUST make sure that "Copy Audio with Project" is checked and choose a new location/folder for the save.
 
If you do this for all of your projects you can safely delete everything in the Global audio folder.