Here is my scenario:
I don't know much about the MediaMuxer but ffmpeg does support overlaying functionality. FFMPEG has various filters one of them is overlay filter. What I understand is you want to overlay an image (i.e. png) on the video, ffmpeg surely is a useful framework to do this job. You can set the output format you can set the co-ordinates of the image which is to be overplayed.
E.g.
ffmpeg -i input.avi -i logo.png -filter_complex 'overlay=10:main_h-overlay_h-10' output.avi
Above command adds overlays logo.png on the input.avi video file in bottom left corner.
More information about the filters is available at following website,
https://www.ffmpeg.org/ffmpeg-filters.html#overlay-1
If this is a solution to your problem you need the C code equivalent to the above command. You also need to see the performance of the ffmpeg because it a pure software framework.
Hope I have understood your question correctly and this helps.
If you need do this without ffmpeg on Android device:
Start from : https://github.com/google/grafika
The answer on your question between Play video (PlayMovieActivity.java) and Record Gl App (RecordFBOActivity.java) examples.
Steps:
Setup mInputWindowSurface as Video Encoder Input Surface.
Decode frame from video stream using MoviePlayer as video (external) texture.
Draw this video texture on Surface.
Draw watermark on the same Surface over video texture.
Notify MediaCodec that surface ready for encoding:
mVideoEncoder.frameAvailableSoon();
mInputWindowSurface.setPresentationTime(timeStampNanos);
and then goto Step 2.
Don't forget to adjust speed of decoding. Just remove SpeedControlCallback
which in example set to decode 60 FPS video.
Advantages of this way:
Media Codec use hardware decoder/encoder for video processing.
You can change bit rate of result video.
This is what worked for me:
ffmpeg -i input.avi -i logo.png -filter_complex 'overlay=10:main_h-overlay_h-10' -strict -2 output.avi
ffmpeg recommended the usage -strict -2
inorder to allow the usage of experimental codecs. without the inclusion, the accepted answer above fails to work.
You can try INDE Media Pack - https://software.intel.com/en-us/articles/intel-inde-media-pack-for-android-tutorials
It has transcoding\remuxing functionality as MediaComposer class and several sample effects like JpegSubstituteEffect - it shows how substitute video frame by a picture from jpg file and TextOverlayEffect to overlay text on video frame etc. It could be easily enhanced to watermark effect