Hi all. The actual question specified in the header.
ffmpeg -i source.mp4 -acodec copy-b 500k -vf "movie=logo.png [logo]; [in][logo] overlay=0:0 [out]" out.mp4
Gives me a video in which, do watermark, but the transparent background is replaced with black.
If there is some other tool which will not be dancing, — please advise.
If CUDA support — all wonderful :)