Okay, so this is the solution?
Code:
ffmpeg -i video.flv -i audio.mp3 -c copy out.flv -async 1
My 2nd question is: Is there also a solution for first demuxing the video? I muxed them with mencoder.exe.
Now I'd like to write a batch file, that first splits the audio and video, and after that muxes it again via the code you told me.