<p>Let's compile a list of tips.</p>

<p>(Understandably there will be some subjectivity involved, but some pointers would be useful to someone overwhelmed by tackling a large project within the Flash framework.)</p>

These are just scattered thoughts on organization for projects being worked on mostly with the Flash IDE.
First, I highly recommend using source control, like Subversion, CVS, or Git.
Organization of filesystem folder structure is subjective, but I generally have a "src" folder for all my source FLAs and AS class files, and a "deploy" or "bin" folder for compiled files. The src folder would contain class package files, with class packages organized in reverse domain style (e.g. - com.codehinting.projectname.context ). Modify the publish path of your FLA to publish to the deploy folder by tracing back up using the "../" path segment, for as many levels as needed to trace back from the nesting in the src folder.
Also, I typically place third-party libraries (that are pretty well "baked") in a separate location and then modify the global classpath in the Flash IDE to point to this location.
Two extremely handy plugins for the Flash IDE are Create Basic Layers and Library Generator, which quickly create your skeleton layer and library folder structure - saves time versus manually creating layers and folders.