[a continuation of this question]
In order to embed resources in a SWF file, I have to add lines to my HXML file. However, since I'm using FlashDevelop, I don't know where to find that. Where should I put stuff I would ordinarily specify in my HXML?
At least in the case of specifying resources, you can do this by specifying a command line argument (right click the project in the Project view, select Properties..., then click Compiler Options > Additional Compiler Options and add it there).