Frustrated with file structure

Back in the day, Aperture would create an "Aperture Library" file and throw all of my photos into the library. Well that was horrible. It made iPhoto look brilliant, because you could simply organize your photos in folders by date. However iPhoto would create proxies (small files for thumbnails) and throw a ton of additional little files into directories and gummed up the whole works.
So Aperture 1.5 appeared to have solved all this, going to a more logical date/file structure format. But I was looking through my hard drive, trying to dump all of my photos off to an external drive for space savings and I'm noticing there are still Aperture library files.
I'm not certain what I'm looking at. Some of my photos appear in directories on the hard drive. Others seem to be jammed into the Aperture library folder. Where do the files really exist, and if I have multiple library files on other drives, how can I get everything synced up?
I like the interface on Aperture, but the file structure seems really illogical. Is there a better management tool anyone would care to recommend?

You're not really supposed to poke around the Aperture file structure - leave it to Aperture to manage. this is especially true if you're not familiar with how it works.
The files in folders on your hard drive are referenced masters; the files in the Aperture Library are either Managed Masters or Versions (note: versions do not exist as actual image files).
Having Aperture manage your photos is so fundamental to Aperture's raison-d'etre, that if you don't like it, you should use something else (which I guess is what you're looking for recommendations for).
As an aside, there is a good reason for having Aperture manage your files - there is a potentially complicated relationship between masters and versions, the albums and slide shows etc that they appear in, that it takes a database to keep track of all of this. If you start moving bits around without telling the DBM (and I'm not saying that you are), don't complain if things break.
You'll find the same approach in large IT companies, managing large volumes of source code - on no account can you update code outside of the source management application. If you do, other bits of related source code may not be re-compiled etc when they should be and your production system comes crashing down.
Regards,
Steve

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    3D105122230377/014143N 191601070012001051222100700040000,4714830047,8638500105
    3D105122221885/014143N 191601073012001051222104500130000,5358330048,0378500106
    3D105122208380/014143N 191601071517001051222122500110000,5779500047,7382700107
    3D105122224171/014143N 191601070011001051222124300081000,6140330047,7543800108
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