I have been placing my assets withing the subdirectory of whatever components/code uses them. This has two benefits: cleaner code and if I ever decide to reuse the code, I only have one directory to copy. Although I would say that for a style for the entire application, you may wish to place this at the root instead of having it scattered about. It depends a lot on the relationship between your skins and your code.
If you have an application that is split up into multiple parts then I usually split it up into sub folders (i.e. com.puremvc.app.forum.view, etc. ). This way packages contain only code relevant to that particular piece of functionality.
A little digression; the package structure isn't usually named after the company/organization but rather the reverse domain name of your website:
The reasoning behind this is that only one individual/organization is associated with a domain name, this helps avoid package naming conflicts.
Of course, this mostly matters if you plan on reusing your code elsewhere/distributing it or are bringing in libraries that having naming conflicts with yours.
Here's a document on Adobe's site explaining it in more detail (it's for AS2, but most of it carries over, package details are near the bottom):http://www.adobe.com/devnet/flash/articles/as_bestpractices_02.html