I don't do it in the process. Whenever I add some flac files to my collection, I also add them manually to a second folder as mp3. That folder goes to my cellphone (Automatically synced with foldersyncpro).
So far using my favorite songs, requires me to heavily edit the exported m3u (file path, unix/windows slashes and of course renaming the flac files to mp3). Everything but the last part is automated now with music bee.