File -> Relocate Masters. You can do that project by project...
Or is there a way to go through aperture to make a new reference library that I can move the masters into later?
you do not move the masters into a references library - you turn your current library into a referenced library. As Terence Devlin said:
File -> Relocate Masters
What you should set up:
- Select a folder, where you want to store your referenced files - probably on an external drive.
- Decide on a hierarchical folder structure inside this folder - that is completely up to you.
- Select a project from your library and use the command "File -> Relocate Masters/Originals" to move the original image files to the folder where you want to go them to. Only take care not to send two projects to the same folder.
Alternatively, if you do not care about the folder structure Aperture will use, select all images at once from the "Photos" view and let Aperture decide how to assing the folders - in the "Relocate Originals" dialoge you can specify a subfolder format.