http://ffmpeg.org/ffmpeg-filters.html#toc-Examples-54Code:Insert 2 different transparent PNG logos (second logo on bottom right corner) using the ffmpeg tool: ffmpeg -i video.mp4 -i logo1.png -i logo2.png -filter_complex 'overlay=x=10:y=H-h-10,overlay=x=W-w-10:y=H-h-10' output.mp4
Maybe you could add everything in the -vf command also...but I'm not sure how.