How to handle images stored /outside/ Aperture

I am coming from a PC environment where my images were stored all over my hard drive in various folders and subfolders. I am part-way through organizing all of this in Aperture but I OFTEN find myself exporting images to folders on my desktop in order to upload them to FTP or edit them in Photoshop conveniently and as I move to working in something like an Adobe Suite that allows me to edit and link images I do see myself keeping images outside of Aperture.
Can anyone help me out with how to manage this a little more practically (say by only keeping images on the desktop but not in the Documents Folder) and/or should I be trying to discipline myself down to keeping everything in Aperture? I find it relatively confusing to do it this way but am very interested in getting some advice on this.
Thanks,
Jon

Jon,
I used to have everything sorted with the top folder being 'Project 1', 'Project 2', 'Project 3', etc. with either all files in that folder, or sub-folders for each file type. This was pretty good, but eventually got out of hand once I had a couple hundred projects with all types of files in each folder and needed to find a specific file (say an Illustrator file I needed to work on).
Now, I use the following structure for Adobe CS5 projects:
Top level folder = 'Design Files'
Second level folders = 'Photoshop Files', 'Illustrator Files', 'InDesign Files', 'Acrobat Files'
Third level folders (inside each of the second level folders as needed) = 'Project 1', 'Project 2', 'Project 3', etc.
This gives me all my PSD files inside one master 'Photoshop Files' folder divided by Project folders. If - for example - Project 1 has PSD files, AI files, IND files and PDF files, then there is a Project 1 folder under each of the second level folders for each program. This allows me easy access to either all files for a program by going to that folder, or I can run a dynamic search (smart folder) for a project and see all relevant folders for that project in the search results.
The main reason I have it this way now is that I usually remember the file type (as mentioned above for an Illustrator file). I typically remember that I did an illustration, but can't remember the file name of the illustration or the project it went in for sure. My current structure shortens my search time considerably.
Note - I can also use Bridge CS5 very easily for the Adobe CS5 files since it shows thumbnails of the actual file and I can visually search very fast that way.
At home - with Aperture - I only hold the original images (pictures) that I started to work with. I don't keep any PSD, TIFF, PDF, PNG, etc. in the library. This is simply because Bridge is much better at showing those files with transparency if it exists, and Aperture stays a straight-forward image (picture) database for me.
If I send an image to a plug-in or to Photoshop from inside Aperture, I do it for a specific purpose and then I complete the process and export it to one of the dedicated folders in Finder (typically to my Photoshop Files folder). If I really need to keep the layer work in a PSD file, then I will use the 'Save As' command from inside Photoshop to save out to a folder and then just trash the file Aperture sent to Photoshop. Although I have not had any real issues with Aperture holding PSD files in the past, I simply trust Adobe to handle their own files without relying on Apple's program to do it for me.
As far as miscellaneous files (screenshots, scans, web icons), I really don't do many of those. I have a few scans which are not part of any project and just keep those in a two level folder (Art / Scans). For web icons, I would probably suggest going with the program you used for a folder (Photoshop Files?). Not sure what program or file type you are using for those (GIF, PNG - I don't work with web design so not real familiar with current practices for icon design for the web).
For JPEG files, I use a second level 'JPEG files' folder for any JPEG's that are used in my design projects in a 'Project 1', 'Project 2', etc. folder (same as the other file types mentioned above). Although, I typically use PSD files as source files and then save out JPEG's on a case-by-case basis (similar to using Aperture as the source and exporting as needed).
Since most of my design files are for InDesign projects, I complete the project by embedding all links in the document after having printed to PDF (and proof-reading prior to embedding). This protects against lost links if I need to work with the master file again for some reason. I can always place a new image or file in the document as needed and since I have a PDF of the file to send to collegues, the extra file size in the InDesign file after embedding is not a big deal.
So, in summary; I use a top level folder (based on category; e.g., Design Files) and then organize by file type parent folders with dedicated project folders under those as needed. Works for the way I think.
I hope that was somewhat clear.
Message was edited by: CorkyO2 to change "top level file" to "top level folder" in summary.

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