ffmpeg split screen two video sources
If you're using filter_complex, then all filtering has to happen within that complex. So,

ffmpeg.exe -f dshow -i video="screen-capture-recorder" \
           -f dshow -i video="Microsoft LifeCam HD-6000" \
-filter_complex "[0:v]crop=1280:360:0:0[v0];[1:v]crop=1280:360:0:0[v1];[v0][v1]vstack[v]" \
-map [v] -vcodec libx264 -pix_fmt yuv420p -preset ultrafast 6000screen_take1.mkv


This stacks the top half of the webcam video below the top half of the desktop capture.



Having taken a look at the console output, you should actually try this:

ffmpeg.exe -f dshow -rtbufsize 9000000 -i video="screen-capture-recorder" \
           -f dshow -i video="Microsoft LifeCam HD-6000" \
-filter_complex "[0:v]crop=1280:360:0:0[v0];[1:v]scale=1280:-1,crop=1280:360:0:0[v1]; \
                 [v0][v1]vstack[v]" \
-map [v] -vcodec libx264 -pix_fmt yuv420p -preset ultrafast 6000screen_take1.mkv