Basta combiná-los:
ffmpeg -f v4l2 -framerate 25 -video_size 640x480 -i /dev/video0 \
-f x11grab -framerate 100 -video_size 1600x900 -i :0.0 \
-filter_complex "[0:v]pad=iw:900:0:(oh-ih)/2[left];[left][1:v]hstack,format=yuv420p" \
-c:v libx264 -f segment -segment_time 1 -strftime 1 '%Y-%m-%d_%H-%M-%S.ts'