export your movie to flv and in the setting set On2 (and not sorenson)
Or you can use an h264 file, but i guess it will require more work to have it play inside your flash.
Not sure I'm 100% on this:
If you export as FLV with On2 you can preserve alpha transparencies (if you want any of the SWF background to show through).
If you export as h.264 and try to import into Flash (under File>Import) it will likely try to convert it to FLV/F4V -- that is if you are loading it into the library. You can load h.264 in via the Netstream Actionscript class. I'm not sure if you can load it into an instance of the FLV Player component. I think that may be possible -- I'm pretty sure you cannot embed H.264 directly into the timeline, though, so you need something that "loads in" the seperate H.264 file.
If your movie is short enough (or small enough, dimensionally -- or both) you may want to consider rendering your movie as a series of frame images, then importing the series of frames directly onto the timeline of a new movieclip. The resultant SWF size (in kb) then becomes the main concern. If you go this route, 24bit PNG files also retain their Alpha values if that is important to you. Depends on what you are after. Embedding is probably best if your are adding effects to your flash movie, not full movies that are "standalone" inside the SWF.