Suppose you are given a folder with these 5 things in it:
I am right now just creating a .fla called ProjectNameShell.fla that is basically an empty file. I just use it to publish through CS6 and also state which class to start from. Is the standard place to put this fla in this first folder or in src?
Looks like a FlashDevelop project. In that I'd put FLA and project-specific classes in /src. Any 3rd party code in /lib. Publish to /bin. /obj is the wildcard, which could be complex objects (3d, etc). Some people choose to keep the FLA in the root folder (not in any of those folders) and leave /src to just project-specific code (mostly for easy repository usage).
There's no "perfect" way to do it. Just be on the same page with the people you work with.