Go to "Project > New Project".
Select Flex 3 Project.
For the name, enter "FlashSDK", the location doesn't matter - memorize it though. Make sure to check "Create directory for project".
After that's done, locate the /src/ directory in the *actual* Flash SDK, and drag&drop it onto the src directory in the project tree in FlashDevelop. It should take a while, but now your files are be copied and in the project.
You can delete Main.mxml from the src directory. Then, right-click RuntimeFlash.mxml and check "Always compile" (It will be the entry point).
Now, try Project > Build.
If you have to set a Flex SDK location, choose MMF2\Data\Runtime\Flash\Flex\.
Try again - it should now build, but with errors.
If one of the errors is:
you're done. It just means that there's no application for debugging.
Error: unable to resolve 'Application.ccf' for transcoding
As mentioned in the PDF, make a new application in MMF, set the build type to SWF. Then, go to File > Build > Application, locate the /src/ directory of your project, enter whatever you want for the file name, hold SHIFT and press OK. Now, try building again. It should work.