Apache – Which version of Flex Builder do I need

Generally, you are correct: Using FlexBuilder the idea is that you will create a project that has a single thing to be built (.swf, .swc, etc).

A file repository (as you mentioned you use) is definitely a MUST HAVE for large-scale development.

Adding build tools such as Ant (my personal favorite) and Maven (growing in popularity and ability pretty quickly) to your toolbox allow you to do more advanced building (and even unit-testing). These types of tools will allow the building of a large application with many aspects and dependencies in a single action. This is a must for large-scale applications and development environments. For larger projects with a lot of sub-projects I will often have a single "master" project that is little more than a build script that calls sub-project build scripts and puts everything together. Maven is particularly good at that. There are Eclipse plug-ins that help out with both of those tools.

Different situations require different ways to use the projects together. It may be helpful to directly link to a Library project as a dependency. That way your projects are able to debug the linked code and modify it as needed. Or if library projects are less commonly modified then their assets could be dropped into the /libs folder of the dependant project eliminating the need to have the .swc generating project open while development goes on.

Keeping your projects to a one-asset-per-project situation goes a long way to keeping it organized. Generally I have a folder for each client and in there a folder for each project. If that project needs to be broken down into sub-projects then ALL of those sub-projects will be located in that project folder (no matter what the relationship is to each other).

Sometimes it is of course helpful to have a number of assets be created for a single project. This could be multiple .swfs for different situations, different .zips for distribution to different places or clients or a dozen other situations. "Asset" projects are sometimes a good example of this. Sometimes I have a "project" that is just my collection of assets. I don't normally access this project from within FlexBuilder and it doesn't normally have the .project and other Eclipse files.