Aperture No Longer finds Masters

Question

I have a large number of my photos that I have opened and worked with in Photoshop adding layers and such.
Within Aperture, these files show that they are a PSD file.  But now when I choose to edit them in photoshop, all the layers are gone.
I found the original Masters (with layers) within my Aperture Library on the hard drive (I chose to Show Package Contents).
The file is there as a PSD file and when I open it from the finder it opens in Photoshop with layers in tact.
It seems a big mess.  For many of the files there are multiple PSD files (taking up a lot of room).  And there are even folders within folders with the same file name and even more .psd files.
It's a nightmare.
A few questions:
1) How do I get Aperture to display the original master so that when I view it in Aperture and then choose to edit it in Photoshop, that it is the version with layers?  Basically, How do I get Aperture to cull through it's own Masters Files and correctly show them in Aperture?
2) How do I clean up all the duplicates upon duplicates within the Aperture Masters files?
I have done a complete rebuild of the Library.  And I think that has actually created a lot of these duplicates.
Help!!

Answer 1

Note that if you import a PSD file into Aperture, and then choose "Open in..." from within Aperture to open it in Photoshop, it will flatten the image.  That's the way things work.  The first time "Open in..." is used from Aperture it "renders" its version which is flattened.  So if you have multi-layer PSD files outside Aperture that originally started with Camera RAW or something, you may want to leave them outside of Aperture.
The best way to work is to start with the RAW files in Aperture and use it to manage them.  You do "Open in..." to Photoshop or other external editor near the end of the process.