mitch, here's how i addressed my switch between Lightroom and Aperture 2.
but before i continue, one of the key feature that attracted me to Lightroom is that it doesn't package my imports into a single file like Aperture does. since LR doesn't do this, it offers its users an automated feature where it will automatically organize the imported images based on capture year, month, and date. this option is sorely missing in Aperture. anyway, my Lightroom folder structure is automatically like this:
YYYY > MM > DD
this is good when i need to start archiving to DVD because i can easily break up the collection into different year, month, and date.
now on to Aperture 2: since Aperture doesn't automatically structure my images as Lightroom does while they're imported, i have to manually do the following so that the structure makes sense to me. also, i want to imitate the same folder structure defined by Lightroom so that if i decide to import and store files in their current location, or if i want to continue using Lightroom for other things, i can easily keep track of the images' physical location:
YYYY (folder) > MM (folder) > YYYY-MM-DD (project)
the reason the project is named in YYYY-MM-DD format is for archiving purposes. over time, your Aperture Library will become quite large because of new images, and edits. to help keep the library file size manageable, i export idle projects and burn them to DVD. then, i delete the archived project(s) from the library.
an advantage with this structure is that, when you select the YYYY folder, Aperture will display all the images filed inside this folder. if you wish to see all the images for MM folder, then you select this folder. if you wish to see the images for a specific date, then you select a project named, YYYY-MM-DD. you can go further and create folder(s) inside a project.
i hope this made sense, and was helpful to you.
EDIT: oops, i didn't answer your question. where the raw file is stored depends on your import option. at import, you have the option to store files in the Aperture Library, in their current location, in Pictures folder, or Choose another location. if you choose the first option, in the Aperture Library, then your raw files will be packaged in this library. if you choose the second option, then your raw files will remain where they are. however, versions will be stored in the Aperture Library. note that if you're importing from Lightroom, even Lightroom's Versions are treated as Masters in Aperture.